1
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Aliakbari M, Karkhane AA. In vivo cloning of PCR product via site-specific recombination in Escherichia coli. Appl Microbiol Biotechnol 2024; 108:400. [PMID: 38951186 PMCID: PMC11217044 DOI: 10.1007/s00253-024-13239-7] [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: 03/25/2024] [Revised: 06/02/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024]
Abstract
Over the past years, several methods have been developed for gene cloning. Choosing a cloning strategy depends on various factors, among which simplicity and affordability have always been considered. The aim of this study, on the one hand, is to simplify gene cloning by skipping in vitro assembly reactions and, on the other hand, to reduce costs by eliminating relatively expensive materials. We investigated a cloning system using Escherichia coli harboring two plasmids, pLP-AmpR and pScissors-CmR. The pLP-AmpR contains a landing pad (LP) consisting of two genes (λ int and λ gam) that allow the replacement of the transformed linear DNA using site-specific recombination. After the replacement process, the inducible expressing SpCas9 and specific sgRNA from the pScissors-CmR (CRISPR/Cas9) vector leads to the removal of non-recombinant pLP-AmpR plasmids. The function of LP was explored by directly transforming PCR products. The pScissors-CmR plasmid was evaluated for curing three vectors, including the origins of pBR322, p15A, and pSC101. Replacing LP with a PCR product and fast-eradicating pSC101 origin-containing vectors was successful. Recombinant colonies were confirmed following gene replacement and plasmid curing processes. The results made us optimistic that this strategy may potentially be a simple and inexpensive cloning method. KEY POINTS: •The in vivo cloning was performed by replacing the target gene with the landing pad. •Fast eradication of non-recombinant plasmids was possible by adapting key vectors. •This strategy is not dependent on in vitro assembly reactions and expensive materials.
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Affiliation(s)
- Moein Aliakbari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ali Asghar Karkhane
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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2
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Li S, Tan W, Jia X, Miao Q, Liu Y, Yang D. Recent advances in the synthesis of single-stranded DNA in vitro. Biotechnol J 2024; 19:e2400026. [PMID: 38622795 DOI: 10.1002/biot.202400026] [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: 01/11/2024] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024]
Abstract
Single-stranded DNA (ssDNA) is the foundation of modern biology, with wide applications in gene editing, sequencing, DNA information storage, and materials science. However, synthesizing ssDNA with high efficiency, high throughput, and low error rate in vitro remains a major challenge. Various methods have been developed for ssDNA synthesis, and some significant results have been achieved. In this review, six main methods were introduced, including solid-phase oligonucleotide synthesis, terminal deoxynucleotidyl transferase-based ssDNA synthesis, reverse transcription, primer exchange reaction, asymmetric polymerase chain reaction, and rolling circle amplification. The advantages and limitations of each method were compared, as well as illustrate their representative achievements and applications. Especially, rolling circle amplification has received significant attention, including ssDNA synthesis, assembly, and application based on recent work. Finally, the future challenges and opportunities of ssDNA synthesis were summarized and discussed. Envisioning the development of new methods and significant progress will be made in the near future with the efforts of scientists around the world.
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Affiliation(s)
- Shuai Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Wei Tan
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Xuemei Jia
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Qing Miao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Ying Liu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
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3
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Chin WC, Zhou YZ, Wang HY, Feng YT, Yang RY, Huang ZF, Yang YL. Bacterial polyynes uncovered: a journey through their bioactive properties, biosynthetic mechanisms, and sustainable production strategies. Nat Prod Rep 2024. [PMID: 38284321 DOI: 10.1039/d3np00059a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Covering: up to 2023Conjugated polyynes are natural compounds characterized by alternating single and triple carbon-carbon bonds, endowing them with distinct physicochemical traits and a range of biological activities. While traditionally sourced mainly from plants, recent investigations have revealed many compounds originating from bacterial strains. This review synthesizes current research on bacterial-derived conjugated polyynes, delving into their biosynthetic routes, underscoring the variety in their molecular structures, and examining their potential applications in biotechnology. Additionally, we outline future directions for metabolic and protein engineering to establish more robust and stable platforms for their production.
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Affiliation(s)
- Wei-Chih Chin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yang-Zhi Zhou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Hao-Yung Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Department of Wood Based Materials and Design, National Chiayi University, Chiayi, Taiwan
| | - Yu-Ting Feng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Ru-Yin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Zih-Fang Huang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
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4
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Su T, Pang Q, Qi Q. In Vivo DNA Assembly Using the PEDA Method. Methods Mol Biol 2024; 2760:437-445. [PMID: 38468102 DOI: 10.1007/978-1-0716-3658-9_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Simple and efficient DNA assembly methods have been widely used in synthetic biology. Here, we provide the protocol for the recently developed PEDA (phage enzyme-assisted in vivo DNA assembly) method for direct in vivo assembly of individual DNA parts in multiple microorganisms, such as Escherichia coli, Ralstonia eutropha, Pseudomonas putida, Lactobacillus plantarum, and Yarrowia lipolytica. PEDA allows in vivo assembly of DNA fragments with homologous sequences as short as 5 bp, and the efficiency is comparable to the prevailing in vitro DNA assembly, which will broadly boost the rapid progress of synthetic biology.
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Affiliation(s)
- Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Qingxiao Pang
- Shandong Lishan Biotechnology Co. LTD, Jinan, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China.
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5
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He B, Ma Y, Tian F, Zhao GR, Wu Y, Yuan YJ. YLC-assembly: large DNA assembly via yeast life cycle. Nucleic Acids Res 2023; 51:8283-8292. [PMID: 37486765 PMCID: PMC10450165 DOI: 10.1093/nar/gkad599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023] Open
Abstract
As an enabling technique of synthetic biology, the scale of DNA assembly largely determines the scale of genetic manipulation. However, large DNA assembly technologies are generally cumbersome and inefficient. Here, we developed a YLC (yeast life cycle)-assembly method that enables in vivo iterative assembly of large DNA by nesting cell-cell transfer of assembled DNA in the cycle of yeast mating and sporulation. Using this method, we successfully assembled a hundred-kilobase (kb)-sized endogenous yeast DNA and a megabase (Mb)-sized exogenous DNA. For each round, over 104 positive colonies per 107 cells could be obtained, with an accuracy ranging from 67% to 100%. Compared with other Mb-sized DNA assembly methods, this method exhibits a higher success rate with an easy-to-operate workflow that avoid in vitro operations of large DNA. YLC-assembly lowers the technical difficulty of Mb-sized DNA assembly and could be a valuable tool for large-scale genome engineering and synthetic genomics.
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Affiliation(s)
- Bo He
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Yuan Ma
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Fangfang Tian
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Guang-Rong Zhao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Yi Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
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6
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Salazar-Cerezo S, de Vries RP, Garrigues S. Strategies for the Development of Industrial Fungal Producing Strains. J Fungi (Basel) 2023; 9:834. [PMID: 37623605 PMCID: PMC10455633 DOI: 10.3390/jof9080834] [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: 06/12/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed.
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Affiliation(s)
- Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Sandra Garrigues
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, VLC, Spain
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7
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Ni X, Liu Z, Guo J, Zhang G. Development of Terminator-Promoter Bifunctional Elements for Application in Saccharomyces cerevisiae Pathway Engineering. Int J Mol Sci 2023; 24:9870. [PMID: 37373018 DOI: 10.3390/ijms24129870] [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: 12/15/2022] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
The construction of a genetic circuit requires the substitution and redesign of different promoters and terminators. The assembly efficiency of exogenous pathways will also decrease significantly when the number of regulatory elements and genes is increased. We speculated that a novel bifunctional element with promoter and terminator functions could be created via the fusion of a termination signal with a promoter sequence. In this study, the elements from a Saccharomyces cerevisiae promoter and terminator were employed to design a synthetic bifunctional element. The promoter strength of the synthetic element is apparently regulated through a spacer sequence and an upstream activating sequence (UAS) with a ~5-fold increase, and the terminator strength could be finely regulated by the efficiency element, with a ~5-fold increase. Furthermore, the use of a TATA box-like sequence resulted in the adequate execution of both functions of the TATA box and the efficiency element. By regulating the TATA box-like sequence, UAS, and spacer sequence, the strengths of the promoter-like and terminator-like bifunctional elements were optimally fine-tuned with ~8-fold and ~7-fold increases, respectively. The application of bifunctional elements in the lycopene biosynthetic pathway showed an improved pathway assembly efficiency and higher lycopene yield. The designed bifunctional elements effectively simplified pathway construction and can serve as a useful toolbox for yeast synthetic biology.
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Affiliation(s)
- Xiaoxia Ni
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China
| | - Zhengyang Liu
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China
| | - Jintang Guo
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China
| | - Genlin Zhang
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China
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8
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Gurdo N, Volke DC, McCloskey D, Nikel PI. Automating the design-build-test-learn cycle towards next-generation bacterial cell factories. N Biotechnol 2023; 74:1-15. [PMID: 36736693 DOI: 10.1016/j.nbt.2023.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023]
Abstract
Automation is playing an increasingly significant role in synthetic biology. Groundbreaking technologies, developed over the past 20 years, have enormously accelerated the construction of efficient microbial cell factories. Integrating state-of-the-art tools (e.g. for genome engineering and analytical techniques) into the design-build-test-learn cycle (DBTLc) will shift the metabolic engineering paradigm from an almost artisanal labor towards a fully automated workflow. Here, we provide a perspective on how a fully automated DBTLc could be harnessed to construct the next-generation bacterial cell factories in a fast, high-throughput fashion. Innovative toolsets and approaches that pushed the boundaries in each segment of the cycle are reviewed to this end. We also present the most recent efforts on automation of the DBTLc, which heralds a fully autonomous pipeline for synthetic biology in the near future.
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Affiliation(s)
- Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Douglas McCloskey
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark.
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9
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Liu L, Huang Y, Wang HH. Fast and efficient template-mediated synthesis of genetic variants. Nat Methods 2023:10.1038/s41592-023-01868-1. [PMID: 37127666 DOI: 10.1038/s41592-023-01868-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
Abstract
Efficient methods for the generation of specific mutations enable the study of functional variations in natural populations and lead to advances in genetic engineering applications. Here, we present a new approach, mutagenesis by template-guided amplicon assembly (MEGAA), for the rapid construction of kilobase-sized DNA variants. With this method, many mutations can be generated at a time to a DNA template at more than 90% efficiency per target in a predictable manner. We devised a robust and iterative protocol for an open-source laboratory automation robot that enables desktop production and long-read sequencing validation of variants. Using this system, we demonstrated the construction of 31 natural SARS-CoV2 spike gene variants and 10 recoded Escherichia coli genome fragments, with each 4 kb region containing up to 150 mutations. Furthermore, 125 defined combinatorial adeno-associated virus-2 cap gene variants were easily built using the system, which exhibited viral packaging enhancements of up to 10-fold compared with wild type. Thus, the MEGAA platform enables generation of multi-site sequence variants quickly, cheaply, and in a scalable manner for diverse applications in biotechnology.
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Affiliation(s)
- Liyuan Liu
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Yiming Huang
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
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10
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Venken KJ, Matinyan N, Gonzalez Y, Sarrion-Perdigones A, Dierick HA. Synthetic Assembly DNA Cloning to Build Plasmids for Multiplexed Transgenic Selection, Counterselection or Any Other Genetic Strategies Using Drosophila melanogaster. Curr Protoc 2023; 3:e653. [PMID: 36757602 PMCID: PMC10281009 DOI: 10.1002/cpz1.653] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We recently described a drug-based selectable and counterselectable genetic platform for the animal model system Drosophila melanogaster, consisting of four resistance and two sensitivity markers that allow direct selection for, or counterselection against, a desired genotype. This platform eliminates the need to identify modified progeny by traditional laborious screening using the dominant eye and body color markers, white+ and yellow+ , respectively. The four resistance markers permit selection of animals using G418 sulfate, puromycin HCl, blasticidin S, or hygromycin B, while the two sensitivity markers allow counterselection of animals against ganciclovir or acyclovir and 5-fluorocytosine. The six markers can be used alone or in combination to perform co-selection, combination selection, and counterselection, as well as co-counterselection. To make this novel selection and counterselection genetics platform easily accessible to and rapidly implementable by the scientific community, we used a synthetic assembly DNA cloning platform, GoldenBraid 2.0 (GB2.0). GB2.0 relies on two Type IIs restriction enzymes that are alternatingly used during successive cloning steps to make increasingly complex genetic constructs. Here we describe, as an example, how to perform synthetic assembly DNA cloning using GB2.0 to build such complex plasmids via the assembly of both components of the binary LexA/LexA-Op overexpression system, a G418 sulfate-selectable LexA transactivator plasmid, and a blasticidin S-selectable LexA-Op responder plasmid. We demonstrate the functionality of these plasmids by including the expression pattern obtained after co-injection, followed by co-selection using G418 sulfate and blasticidin S, resulting in co-transgenesis of both plasmids. Protocols are provided on how to obtain, adapt, and clone DNA parts for synthetic assembly cloning after de novo DNA synthesis or PCR amplification of desired DNA parts and how to assemble those DNA parts into multipartite transcription units, followed by how to further assemble multiple transcription units into genetic constructs of increasing complexity to perform multiplexed transgenic selection and counterselection, or any other genetic strategies using Drosophila melanogaster. The protocols we present can be easily adapted to incorporate any of the six selectable and counterselectable markers, or any other, markers, to generate plasmids of unmatched complexity for various genetic applications. A protocol on how to generate transgenic animals using these synthetically assembled plasmids is described in an accompanying Current Protocols article (Venken, Matinyan, Gonzalez, & Dierick, 2023). © 2023 Wiley Periodicals LLC. Basic Protocol 1: Obtaining and cloning a de novo-synthesized DNA part for synthetic assembly DNA cloning Basic Protocol 2: Obtaining and cloning a DNA part amplified by PCR from existing DNA resources for synthetic assembly DNA cloning Alternate Protocol: Obtaining, adapting, and cloning a DNA part amplified by PCR from existing DNA resources for synthetic assembly DNA cloning Basic Protocol 3: Synthetic assembly DNA cloning of individual DNA parts into a multipartite transcription unit Basic Protocol 4: Synthetic assembly DNA cloning of multiple transcription units into genetic constructs of increasing complexity.
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Affiliation(s)
- Koen J.T. Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nick Matinyan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Herman A. Dierick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
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11
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An Optimized Transformation Protocol for Escherichia coli BW3KD with Supreme DNA Assembly Efficiency. Microbiol Spectr 2022; 10:e0249722. [PMID: 36317996 PMCID: PMC9769673 DOI: 10.1128/spectrum.02497-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
DNA cloning requires two steps: the assembly of recombinant DNA molecules and the transformation of the product into a host organism for replication. High efficiencies in both processes can increase the success rate. Recently, we developed an Escherichia coli BW3KD strain with higher transformation efficiency than commonly used cloning strains. Here, we further developed a simple method named TSS-HI (transformation storage solution optimized by Hannahan and Inoue method) for competent cell preparation, which combined the advantages of three common methods for operational simplicity and high transformation efficiency. When competent BW3KD cells were prepared using this developed method, the transformation efficiency reached up to (7.21 ± 1.85) × 109 CFU/μg DNA, which exceeded the levels of commercial chemically competent cells and homemade electrocompetent cells. BW3KD cells formed colonies within 7 h on lysogeny broth agar plates, quicker than the well-known fast-growing E. coli cloning strain Mach1. The competent cells worked effectively for the transformation of assembled DNA of 1 to 7 fragments in one step and promoted efficiencies of transformation or cloning with large plasmids. The cloning efficiency of BW3KD cells prepared by this method increased up to 828-fold over that of E. coli XL1-Blue MRF' cells prepared by a common method. Thus, competent cells are suitable for different cloning jobs and should help with the increased demand for DNA assembly in biological studies and biotechnology. IMPORTANCE DNA transformation is commonly used in cloning; however, high transformation efficiency becomes a limiting factor in many applications, such as the construction of CRISPR and DNA libraries, the assembly of multiple fragments, and the transformation of large plasmids. We developed a new competent cell preparation method with unmatched transformation efficiency. When the BW3KD strain, derived from Escherichia coli BW25113 cells, was prepared by this method, its transformation efficiency reached up to (7.21 ± 1.85) × 109 CFU/μg DNA, which broke the record for chemically prepared competent cells. Routine cloning could be completed in 1 day due to the high growth rate of this strain. The competent cells were shown to be highly efficient for transformation or cloning with large plasmids and for the assembly of multiple fragments. The results highlight the effectiveness of the new protocol and the usefulness of the BW3KD strain as the host.
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PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction. Nat Commun 2022; 13:2697. [PMID: 35577775 PMCID: PMC9110713 DOI: 10.1038/s41467-022-30355-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/28/2022] [Indexed: 01/01/2023] Open
Abstract
Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor-intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error-free construction of plasmids with virtually any sequences in a high throughput manner. This platform consists of a most versatile DNA assembly method using Pyrococcus furiosus Argonaute (PfAgo)-based artificial restriction enzymes, a user-friendly frontend for plasmid design, and a backend that streamlines the workflow and integration with a robotic system. As a proof of concept, we used this platform to generate 101 plasmids from six different species ranging from 5 to 18 kb in size from up to 11 DNA fragments. PlasmidMaker should greatly expand the potential of synthetic biology. Despite their broad utility, design and construction of plasmids remains laborious and time-consuming. Here the authors report a robust, versatile, and automated end-to-end platform that enables scarless construction of virtually any plasmid.
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13
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Davies JA. Synthetic Morphogenesis: introducing IEEE journal readers to programming living mammalian cells to make structures. PROCEEDINGS OF THE IEEE. INSTITUTE OF ELECTRICAL AND ELECTRONICS ENGINEERS 2022; 110:688-707. [PMID: 36590991 PMCID: PMC7614003 DOI: 10.1109/jproc.2021.3137077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Synthetic morphogenesis is a new engineering discipline, in which cells are genetically engineered to make designed shapes and structures. At least in this early phase of the field, devices tend to make use of natural shape-generating processes that operate in embryonic development, but invoke them artificially at times and in orders of a technologist's choosing. This requires construction of genetic control, sequencing and feedback systems that have close parallels to electronic design, which is one reason the field may be of interest to readers of IEEE journals. The other reason is that synthetic morphogenesis allows the construction of two-way interfaces, especially opto-genetic and opto-electronic, between the living and the electronic, allowing unprecedented information flow and control between the two types of 'machine'. This review introduces synthetic morphogenesis, illustrates what has been achieved, drawing parallels wherever possible between biology and electronics, and looks forward to likely next steps and challenges to be overcome.
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Affiliation(s)
- Jamie A Davies
- Professor of Experimental Anatomy at the University of Edinburgh, UK, and a member of the Centre for Mammalian Synthetic Biology at that University
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14
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Yang Y, Yu Q, Wang M, Zhao R, Liu H, Xun L, Xia Y. Escherichia coli BW25113 Competent Cells Prepared Using a Simple Chemical Method Have Unmatched Transformation and Cloning Efficiencies. Front Microbiol 2022; 13:838698. [PMID: 35401484 PMCID: PMC8989280 DOI: 10.3389/fmicb.2022.838698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/01/2022] [Indexed: 11/26/2022] Open
Abstract
Escherichia coli recA− strains are usually used for cloning to prevent insert instability via RecA-dependent recombination. Here, we report that E. coli BW25113 (recA+) competent cells prepared by using a previously reported transformation and storage solution (TSS) had 100-fold or higher transformation efficiency than the commonly used E. coli cloning strains, including XL1-Blue MRF’. The cloning success rates with E. coli BW25113 were 440 to 1,267-fold higher than those with E. coli XL1-Blue MRF’ when several inserts were assembled into four vectors by using a simple DNA assembly method. The difference was in part due to RecA, as the recA deletion in E. coli BW25113 reduced the transformation efficiency by 16 folds and cloning success rate by about 10 folds. However, the transformation efficiency and the cloning success rate of the recA deletion mutant of E. coli BW25113 are still 12- and >48-fold higher than those of E. coli XL1-Blue MRF’, which is a commonly used cloning strain. The cloned inserts with different lengths of homologous sequences were assembled into four vectors and transformed into E. coli BW25113, and they were stably maintained in BW25113. Thus, we recommend using E. coli BW25113 for efficient cloning and DNA assembly.
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Affiliation(s)
- Yuqing Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qiaoli Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Rui Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
- *Correspondence: Luying Xun, Yongzhen Xia,
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Luying Xun, Yongzhen Xia,
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Casas A, Bultelle M, Motraghi C, Kitney R. Removing the Bottleneck: Introducing cMatch - A Lightweight Tool for Construct-Matching in Synthetic Biology. Front Bioeng Biotechnol 2022; 9:785131. [PMID: 35083201 PMCID: PMC8784771 DOI: 10.3389/fbioe.2021.785131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022] Open
Abstract
We present a software tool, called cMatch, to reconstruct and identify synthetic genetic constructs from their sequences, or a set of sub-sequences—based on two practical pieces of information: their modular structure, and libraries of components. Although developed for combinatorial pathway engineering problems and addressing their quality control (QC) bottleneck, cMatch is not restricted to these applications. QC takes place post assembly, transformation and growth. It has a simple goal, to verify that the genetic material contained in a cell matches what was intended to be built - and when it is not the case, to locate the discrepancies and estimate their severity. In terms of reproducibility/reliability, the QC step is crucial. Failure at this step requires repetition of the construction and/or sequencing steps. When performed manually or semi-manually QC is an extremely time-consuming, error prone process, which scales very poorly with the number of constructs and their complexity. To make QC frictionless and more reliable, cMatch performs an operation we have called “construct-matching” and automates it. Construct-matching is more thorough than simple sequence-matching, as it matches at the functional level-and quantifies the matching at the individual component level and across the whole construct. Two algorithms (called CM_1 and CM_2) are presented. They differ according to the nature of their inputs. CM_1 is the core algorithm for construct-matching and is to be used when input sequences are long enough to cover constructs in their entirety (e.g., obtained with methods such as next generation sequencing). CM_2 is an extension designed to deal with shorter data (e.g., obtained with Sanger sequencing), and that need recombining. Both algorithms are shown to yield accurate construct-matching in a few minutes (even on hardware with limited processing power), together with a set of metrics that can be used to improve the robustness of the decision-making process. To ensure reliability and reproducibility, cMatch builds on the highly validated pairwise-matching Smith-Waterman algorithm. All the tests presented have been conducted on synthetic data for challenging, yet realistic constructs - and on real data gathered during studies on a metabolic engineering example (lycopene production).
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Affiliation(s)
- Alexis Casas
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Matthieu Bultelle
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Charles Motraghi
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Richard Kitney
- Department of Bioengineering, Imperial College London, London, United Kingdom
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Currin A, Parker S, Robinson CJ, Takano E, Scrutton NS, Breitling R. The evolving art of creating genetic diversity: From directed evolution to synthetic biology. Biotechnol Adv 2021; 50:107762. [PMID: 34000294 PMCID: PMC8299547 DOI: 10.1016/j.biotechadv.2021.107762] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/21/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022]
Abstract
The ability to engineer biological systems, whether to introduce novel functionality or improved performance, is a cornerstone of biotechnology and synthetic biology. Typically, this requires the generation of genetic diversity to explore variations in phenotype, a process that can be performed at many levels, from single molecule targets (i.e., in directed evolution of enzymes) to whole organisms (e.g., in chassis engineering). Recent advances in DNA synthesis technology and automation have enhanced our ability to create variant libraries with greater control and throughput. This review highlights the latest developments in approaches to create such a hierarchy of diversity from the enzyme level to entire pathways in vitro, with a focus on the creation of combinatorial libraries that are required to navigate a target's vast design space successfully to uncover significant improvements in function.
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Affiliation(s)
- Andrew Currin
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
| | - Steven Parker
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Christopher J Robinson
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S Scrutton
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
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17
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Tenhaef N, Stella R, Frunzke J, Noack S. Automated Rational Strain Construction Based on High-Throughput Conjugation. ACS Synth Biol 2021; 10:589-599. [PMID: 33593066 DOI: 10.1021/acssynbio.0c00599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Molecular cloning is the core of synthetic biology, as it comprises the assembly of DNA and its expression in target hosts. At present, however, cloning is most often a manual, time-consuming, and repetitive process that highly benefits from automation. The automation of a complete rational cloning procedure, i.e., from DNA creation to expression in the target host, involves the integration of different operations and machines. Examples of such workflows are sparse, especially when the design is rational (i.e., the DNA sequence design is fixed and not based on randomized libraries) and the target host is less genetically tractable (e.g., not sensitive to heat-shock transformation). In this study, an automated workflow for the rational construction of plasmids and their subsequent conjugative transfer into the biotechnological platform organism Corynebacterium glutamicum is presented. The whole workflow is accompanied by a custom-made software tool. As an application example, a rationally designed library of transcription factor-biosensors based on the regulator Lrp was constructed and characterized. A sensor with an improved dynamic range was obtained, and insights from the screening provided evidence for a dual regulator function of C. glutamicum Lrp.
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Affiliation(s)
- Niklas Tenhaef
- Institute of Bio- and Geosciences − IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Robert Stella
- Institute of Bio- and Geosciences − IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences − IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences − IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich 52425, Germany
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18
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Tan YQ, Xue B, Yew WS. Genetically Encodable Scaffolds for Optimizing Enzyme Function. Molecules 2021; 26:molecules26051389. [PMID: 33806660 PMCID: PMC7961827 DOI: 10.3390/molecules26051389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
Enzyme engineering is an indispensable tool in the field of synthetic biology, where enzymes are challenged to carry out novel or improved functions. Achieving these goals sometimes goes beyond modifying the primary sequence of the enzyme itself. The use of protein or nucleic acid scaffolds to enhance enzyme properties has been reported for applications such as microbial production of chemicals, biosensor development and bioremediation. Key advantages of using these assemblies include optimizing reaction conditions, improving metabolic flux and increasing enzyme stability. This review summarizes recent trends in utilizing genetically encodable scaffolds, developed in line with synthetic biology methodologies, to complement the purposeful deployment of enzymes. Current molecular tools for constructing these synthetic enzyme-scaffold systems are also highlighted.
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Affiliation(s)
- Yong Quan Tan
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Bo Xue
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Correspondence: ; Tel.: +65-6516-8624
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19
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Coradini ALV, Hull CB, Ehrenreich IM. Building genomes to understand biology. Nat Commun 2020; 11:6177. [PMID: 33268788 PMCID: PMC7710724 DOI: 10.1038/s41467-020-19753-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic manipulation is one of the central strategies that biologists use to investigate the molecular underpinnings of life and its diversity. Thus, advances in genetic manipulation usually lead to a deeper understanding of biological systems. During the last decade, the construction of chromosomes, known as synthetic genomics, has emerged as a novel approach to genetic manipulation. By facilitating complex modifications to chromosome content and structure, synthetic genomics opens new opportunities for studying biology through genetic manipulation. Here, we discuss different classes of genetic manipulation that are enabled by synthetic genomics, as well as biological problems they each can help solve.
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Affiliation(s)
- Alessandro L V Coradini
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Cara B Hull
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA.
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20
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Damalas SG, Batianis C, Martin‐Pascual M, de Lorenzo V, Martins dos Santos VAP. SEVA 3.1: enabling interoperability of DNA assembly among the SEVA, BioBricks and Type IIS restriction enzyme standards. Microb Biotechnol 2020; 13:1793-1806. [PMID: 32710525 PMCID: PMC7533339 DOI: 10.1111/1751-7915.13609] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/22/2020] [Accepted: 05/18/2020] [Indexed: 01/15/2023] Open
Abstract
Robust synthetic biology applications rely heavily on the design and assembly of DNA parts with specific functionalities based on engineering principles. However, the assembly standards adopted by different communities vary considerably, thus limiting the interoperability of parts, vectors and methods. We hereby introduce the SEVA 3.1 platform consisting of the SEVA 3.1 vectors and the Golden Gate-based 'SevaBrick Assembly'. This platform enables the convergence of standard processes between the SEVA platform, the BioBricks and the Type IIs-mediated DNA assemblies to reduce complexity and optimize compatibility between parts and methods. It features a wide library of cloning vectors along with a core set of standard SevaBrick primers that allow multipart assembly and exchange of short functional genetic elements (promoters, RBSs) with minimal cloning and design effort. As proof of concept, we constructed, among others, multiple sfGFP expression vectors under the control of eight RBSs, eight promoters and four origins of replication as well as an inducible four-gene operon expressing the biosynthetic genes for the black pigment proviolacein. To demonstrate the interoperability of the SEVA 3.1 vectors, all constructs were characterized in both Pseudomonas putida and Escherichia coli. In summary, the SEVA 3.1 platform optimizes compatibility and modularity of inserts and backbones with a cost- and time-friendly DNA assembly method, substantially expanding the toolbox for successful synthetic biology applications in Gram-negative bacteria.
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Affiliation(s)
- Stamatios G. Damalas
- Laboratory of Systems and Synthetic BiologyWageningen & Research UniversityStippeneng 4Wageningen6708 WEThe Netherlands
| | - Christos Batianis
- Laboratory of Systems and Synthetic BiologyWageningen & Research UniversityStippeneng 4Wageningen6708 WEThe Netherlands
| | - Maria Martin‐Pascual
- Laboratory of Systems and Synthetic BiologyWageningen & Research UniversityStippeneng 4Wageningen6708 WEThe Netherlands
| | - Victor de Lorenzo
- Systems Biology ProgramNational Center of Biotechnology − CSICMadrid28049Spain
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic BiologyWageningen & Research UniversityStippeneng 4Wageningen6708 WEThe Netherlands
- Lifeglimmer GmbHMarkelstrasse 38Berlin12163Germany
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21
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Dusek J, Plchova H, Cerovska N, Poborilova Z, Navratil O, Kratochvilova K, Gunter C, Jacobs R, Hitzeroth II, Rybicki EP, Moravec T. Extended Set of GoldenBraid Compatible Vectors for Fast Assembly of Multigenic Constructs and Their Use to Create Geminiviral Expression Vectors. FRONTIERS IN PLANT SCIENCE 2020; 11:522059. [PMID: 33193468 PMCID: PMC7641900 DOI: 10.3389/fpls.2020.522059] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Methods for simple and fast assembly of exchangeable standard DNA parts using Type II S restriction enzymes are becoming more and more popular in plant synthetic and molecular biology. These methods enable routine construction of large and complex multigene DNA structures. Two available frameworks emphasize either high cloning capacity (Modular Cloning, MoClo) or simplicity (GoldenBraid, GB). Here we present a set of novel α-level plasmids compatible with the GB convention that extend the ability of GB to rapidly assemble more complex genetic constructs, while maintaining compatibility with all existing GB parts as well as most MoClo parts and GB modules. With the use of our new plasmids, standard GB parts can be assembled into complex assemblies containing 1, 5, 10 and up to theoretically 50 units in each successive level of infinite loop assembly. Assembled DNA constructs can be also combined with conventional binary GB-assemblies (1, 2, 4, 8… units). We demonstrate the usefulness of our framework on single tube assembly of replicating plant expression constructs based on the geminivirus Bean yellow dwarf virus (BeYDV).
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Affiliation(s)
- Jakub Dusek
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague, Czechia
| | - Helena Plchova
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Noemi Cerovska
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Zuzana Poborilova
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Oldrich Navratil
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Katerina Kratochvilova
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Cornelius Gunter
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Raygaana Jacobs
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Inga I. Hitzeroth
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Edward P. Rybicki
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Tomas Moravec
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
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22
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Lee JH, Won HJ, Oh ES, Oh MH, Jung JH. Golden Gate Cloning-Compatible DNA Replicon/2A-Mediated Polycistronic Vectors for Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:559365. [PMID: 33193484 PMCID: PMC7609577 DOI: 10.3389/fpls.2020.559365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/30/2020] [Indexed: 05/31/2023]
Abstract
The expression of multiple proteins and high-throughput vector assembly system are highly relevant in the field of plant genetic engineering and synthetic biology. Deployment of the self-cleaving 2A peptide that mediates polycistronic gene expression has been an effective strategy for multigene expression, as it minimizes issues in coordinated transgene regulation and trait staking in plants. However, efficient vector assembly systems optimized for 2A peptide-mediated polycistronic expression are currently unavailable. Furthermore, it is unclear whether protein expression levels are influenced by the transgene position in the polycistronic expression cassette. In this article, we present Golden Gate cloning-compatible modular systems allowing rapid and flexible construction of polycistronic expression vectors applicable for plants. The genetic modules comprised 2A peptides (T2A and P2A)-linked tricistron expression cassette and its acceptor backbones, named pGO-DV1 and pGO-DV2. While both acceptor backbones were binary T-DNA vectors, pGO-DV2 was specially designed to function as a DNA replicon enhancing gene expression levels. Using the Golden Gate cloning, a set of six tricistronic vectors was constructed, whereby three transgenes encoding fluorescent proteins (mCherry, eYFP, and eGFP) were combinatorially placed along the expression cassette in each of the binary vectors. Transient expression of the construct in tobacco leaves revealed that the expression levels of three fluorescent proteins were comparable each other regardless of the gene positions in the tricistronic expression cassette. pGO-DV2-based constructs were able to increase protein expression level by up to 71%, as compared to pGO-DV1-based constructs.
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Affiliation(s)
- Jae Hoon Lee
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, South Korea
| | - Hyo Jun Won
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, South Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Daejeon, South Korea
| | - Eun-Seok Oh
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Man-Ho Oh
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Je Hyeong Jung
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, South Korea
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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24
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Chen YJ, Cheng YY, Wang W, Tian XJ, Lefever DE, Taft DA, Zhang J, Xing J. Rapid, modular, and cost-effective generation of donor DNA constructs for CRISPR-based gene knock-in. Biol Methods Protoc 2020; 5:bpaa006. [PMID: 32411820 PMCID: PMC7211398 DOI: 10.1093/biomethods/bpaa006] [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: 12/20/2019] [Revised: 03/06/2020] [Accepted: 03/18/2020] [Indexed: 11/24/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing techniques find applications in many fields, such as molecular biology, cancer biology, and disease modeling. In contrast to the knock-out procedure, a key step of CRISPR knock-in experiments is the homology-directed repair process that requires donor constructs as repair templates. Therefore, it is desirable to generate a series of donor templates efficiently and cost-effectively. In this study, we developed a new strategy that combines (i) Gibson assembly reaction, (ii) a linker pair composed of eight in silico screened restriction enzyme sites, and (iii) a hierarchical framework, to remarkably improve the efficiency of producing donor constructs for common genes as well as for the genes containing unbalanced guanine-cytosine content and requiring a selectable marker. Furthermore, the approach provides the ability of inserting additional elements into the donor templates, such as single guide RNA recognition sites that have been reported to enhance the efficiency of homology-directed repair. Conclusively, our modularized process is simple, fast, and cost-effective for making donor constructs and benefits the application of CRISPR knock-in methods.
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Affiliation(s)
- Yi-Jiun Chen
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ya-Yun Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Weikang Wang
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Xiao-Jun Tian
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Daniel E Lefever
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Drug Discovery Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - David A Taft
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jingyu Zhang
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jianhua Xing
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
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25
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Dawe RK. Charting the path to fully synthetic plant chromosomes. Exp Cell Res 2020; 390:111951. [PMID: 32151492 DOI: 10.1016/j.yexcr.2020.111951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
The concepts of synthetic biology have the potential to transform plant genetics, both in how we analyze genetic pathways and how we transfer that knowledge into useful applications. While synthetic biology can be applied at the level of the single gene or small groups of genes, this commentary focuses on the ultimate challenge of designing fully synthetic plant chromosomes. Engineering at this scale will allow us to manipulate whole genome architecture and to modify multiple pathways and traits simultaneously. Advances in genome synthesis make it likely that the initial phases of plant chromosome construction will occur in bacteria and yeast. Here I discuss the next steps, including specific ways of overcoming technical barriers associated with plant transformation, functional centromere design, and ensuring accurate meiotic transmission.
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Affiliation(s)
- R Kelly Dawe
- Department of Genetics and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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26
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Schäfer L, Karande R, Bühler B. Maximizing Biocatalytic Cyclohexane Hydroxylation by Modulating Cytochrome P450 Monooxygenase Expression in P. taiwanensis VLB120. Front Bioeng Biotechnol 2020; 8:140. [PMID: 32175317 PMCID: PMC7056670 DOI: 10.3389/fbioe.2020.00140] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/11/2020] [Indexed: 01/31/2023] Open
Abstract
Cytochrome P450 monooxygenases (Cyps) effectively catalyze the regiospecific oxyfunctionalization of inert C-H bonds under mild conditions. Due to their cofactor dependency and instability in isolated form, oxygenases are preferably applied in living microbial cells with Pseudomonas strains constituting potent host organisms for Cyps. This study presents a holistic genetic engineering approach, considering gene dosage, transcriptional, and translational levels, to engineer an effective Cyp-based whole-cell biocatalyst, building on recombinant Pseudomonas taiwanensis VLB120 for cyclohexane hydroxylation. A lac-based regulation system turned out to be favorable in terms of orthogonality to the host regulatory network and enabled a remarkable specific whole-cell activity of 34 U gCDW -1. The evaluation of different ribosomal binding sites (RBSs) revealed that a moderate translation rate was favorable in terms of the specific activity. An increase in gene dosage did only slightly elevate the hydroxylation activity, but severely impaired growth and resulted in a large fraction of inactive Cyp. Finally, the introduction of a terminator reduced leakiness. The optimized strain P. taiwanensis VLB120 pSEVA_Cyp allowed for a hydroxylation activity of 55 U gCDW -1. Applying 5 mM cyclohexane, molar conversion and biomass-specific yields of 82.5% and 2.46 mmolcyclohexanol gbiomass -1 were achieved, respectively. The strain now serves as a platform to design in vivo cascades and bioprocesses for the production of polymer building blocks such as ε-caprolactone.
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Affiliation(s)
- Lisa Schäfer
- Department of Solar Materials, Helmholtz-Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Rohan Karande
- Department of Solar Materials, Helmholtz-Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz-Centre for Environmental Research-UFZ, Leipzig, Germany
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27
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Conde-Pueyo N, Vidiella B, Sardanyés J, Berdugo M, Maestre FT, de Lorenzo V, Solé R. Synthetic Biology for Terraformation Lessons from Mars, Earth, and the Microbiome. Life (Basel) 2020; 10:E14. [PMID: 32050455 PMCID: PMC7175242 DOI: 10.3390/life10020014] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/27/2020] [Accepted: 02/03/2020] [Indexed: 12/17/2022] Open
Abstract
What is the potential for synthetic biology as a way of engineering, on a large scale, complex ecosystems? Can it be used to change endangered ecological communities and rescue them to prevent their collapse? What are the best strategies for such ecological engineering paths to succeed? Is it possible to create stable, diverse synthetic ecosystems capable of persisting in closed environments? Can synthetic communities be created to thrive on planets different from ours? These and other questions pervade major future developments within synthetic biology. The goal of engineering ecosystems is plagued with all kinds of technological, scientific and ethic problems. In this paper, we consider the requirements for terraformation, i.e., for changing a given environment to make it hospitable to some given class of life forms. Although the standard use of this term involved strategies for planetary terraformation, it has been recently suggested that this approach could be applied to a very different context: ecological communities within our own planet. As discussed here, this includes multiple scales, from the gut microbiome to the entire biosphere.
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Affiliation(s)
- Nuria Conde-Pueyo
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain; (B.V.); (M.B.)
- Institut de Biologia Evolutiva, UPF-CSIC, 08003 Barcelona, Spain
| | - Blai Vidiella
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain; (B.V.); (M.B.)
- Institut de Biologia Evolutiva, UPF-CSIC, 08003 Barcelona, Spain
| | - Josep Sardanyés
- Centre de Recerca Matemàtica, Campus UAB Edifici C, 08193 Bellaterra, Barcelona, Spain;
- Barcelona Graduate School of Mathematics (BGSMath), Campus UAB Edifici C, 08193 Bellaterra, Barcelona, Spain
| | - Miguel Berdugo
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain; (B.V.); (M.B.)
- Institut de Biologia Evolutiva, UPF-CSIC, 08003 Barcelona, Spain
- Departamento de Ecología and Instituto Multidisciplinar para el Estudio del Medio “Ramon Margalef”, Universidad de Alicante, Carr. de San Vicente del Raspeig, s/n, 03690 San Vicente del Raspeig, Alicante, Spain;
| | - Fernando T. Maestre
- Departamento de Ecología and Instituto Multidisciplinar para el Estudio del Medio “Ramon Margalef”, Universidad de Alicante, Carr. de San Vicente del Raspeig, s/n, 03690 San Vicente del Raspeig, Alicante, Spain;
| | - Victor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain; (B.V.); (M.B.)
- Institut de Biologia Evolutiva, UPF-CSIC, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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28
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Pollak B, Matute T, Nuñez I, Cerda A, Lopez C, Vargas V, Kan A, Bielinski V, von Dassow P, Dupont CL, Federici F. Universal loop assembly: open, efficient and cross-kingdom DNA fabrication. Synth Biol (Oxf) 2020; 5:ysaa001. [PMID: 32161816 PMCID: PMC7052795 DOI: 10.1093/synbio/ysaa001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/04/2019] [Accepted: 12/23/2019] [Indexed: 01/22/2023] Open
Abstract
Standardized type IIS DNA assembly methods are becoming essential for biological engineering and research. These methods are becoming widespread and more accessible due to the proposition of a 'common syntax' that enables higher interoperability between DNA libraries. Currently, Golden Gate (GG)-based assembly systems, originally implemented in host-specific vectors, are being made compatible with multiple organisms. We have recently developed the GG-based Loop assembly system for plants, which uses a small library and an intuitive strategy for hierarchical fabrication of large DNA constructs (>30 kb). Here, we describe 'universal Loop' (uLoop) assembly, a system based on Loop assembly for use in potentially any organism of choice. This design permits the use of a compact number of plasmids (two sets of four odd and even vectors), which are utilized repeatedly in alternating steps. The elements required for transformation/maintenance in target organisms are also assembled as standardized parts, enabling customization of host-specific plasmids. Decoupling of the Loop assembly logic from the host-specific propagation elements enables universal DNA assembly that retains high efficiency regardless of the final host. As a proof-of-concept, we show the engineering of multigene expression vectors in diatoms, yeast, plants and bacteria. These resources are available through the OpenMTA for unrestricted sharing and open access.
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Affiliation(s)
- Bernardo Pollak
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Fundación Ciencia y Vida, Santiago, Chile
| | - Tamara Matute
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isaac Nuñez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ariel Cerda
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Constanza Lopez
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Valentina Vargas
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Anton Kan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Vincent Bielinski
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Peter von Dassow
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto Milenio de Oceanografía de Chile, Concepción, Chile
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Chris L Dupont
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Fernán Federici
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Santiago, Chile
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29
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Bartley BA, Beal J, Karr JR, Strychalski EA. Organizing genome engineering for the gigabase scale. Nat Commun 2020; 11:689. [PMID: 32019919 PMCID: PMC7000699 DOI: 10.1038/s41467-020-14314-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/18/2019] [Indexed: 12/11/2022] Open
Abstract
Genome-scale engineering holds great potential to impact science, industry, medicine, and society, and recent improvements in DNA synthesis have enabled the manipulation of megabase genomes. However, coordinating and integrating the workflows and large teams necessary for gigabase genome engineering remains a considerable challenge. We examine this issue and recommend a path forward by: 1) adopting and extending existing representations for designs, assembly plans, samples, data, and workflows; 2) developing new technologies for data curation and quality control; 3) conducting fundamental research on genome-scale modeling and design; and 4) developing new legal and contractual infrastructure to facilitate collaboration.
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Affiliation(s)
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, MA, 02138, USA.
| | - Jonathan R Karr
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10128, USA
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30
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Vecchione S, Fritz G. CRIMoClo plasmids for modular assembly and orthogonal chromosomal integration of synthetic circuits in Escherichia coli. J Biol Eng 2019; 13:92. [PMID: 31798686 PMCID: PMC6883643 DOI: 10.1186/s13036-019-0218-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/23/2019] [Indexed: 01/09/2023] Open
Abstract
Background Synthetic biology heavily depends on rapid and simple techniques for DNA engineering, such as Ligase Cycling Reaction (LCR), Gibson assembly and Golden Gate assembly, all of which allow for fast, multi-fragment DNA assembly. A major enhancement of Golden Gate assembly is represented by the Modular Cloning (MoClo) system that allows for simple library propagation and combinatorial construction of genetic circuits from reusable parts. Yet, one limitation of the MoClo system is that all circuits are assembled in low- and medium copy plasmids, while a rapid route to chromosomal integration is lacking. To overcome this bottleneck, here we took advantage of the conditional-replication, integration, and modular (CRIM) plasmids, which can be integrated in single copies into the chromosome of Escherichia coli and related bacteria by site-specific recombination at different phage attachment (att) sites. Results By combining the modularity of the MoClo system with the CRIM plasmids features we created a set of 32 novel CRIMoClo plasmids and benchmarked their suitability for synthetic biology applications. Using CRIMoClo plasmids we assembled and integrated a given genetic circuit into four selected phage attachment sites. Analyzing the behavior of these circuits we found essentially identical expression levels, indicating orthogonality of the loci. Using CRIMoClo plasmids and four different reporter systems, we illustrated a framework that allows for a fast and reliable sequential integration at the four selected att sites. Taking advantage of four resistance cassettes the procedure did not require recombination events between each round of integration. Finally, we assembled and genomically integrated synthetic ECF σ factor/anti-σ switches with high efficiency, showing that the growth defects observed for circuits encoded on medium-copy plasmids were alleviated. Conclusions The CRIMoClo system enables the generation of genetic circuits from reusable, MoClo-compatible parts and their integration into 4 orthogonal att sites into the genome of E. coli. Utilizing four different resistance modules the CRIMoClo system allows for easy, fast, and reliable multiple integrations. Moreover, utilizing CRIMoClo plasmids and MoClo reusable parts, we efficiently integrated and alleviated the toxicity of plasmid-borne circuits. Finally, since CRIMoClo framework allows for high flexibility, it is possible to utilize plasmid-borne and chromosomally integrated circuits simultaneously. This increases our ability to permute multiple genetic modules and allows for an easier design of complex synthetic metabolic pathways in E. coli.
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Affiliation(s)
- Stefano Vecchione
- LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, 35032 Marburg, Germany
| | - Georg Fritz
- LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, 35032 Marburg, Germany
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31
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Currin A, Swainston N, Dunstan MS, Jervis AJ, Mulherin P, Robinson CJ, Taylor S, Carbonell P, Hollywood KA, Yan C, Takano E, Scrutton NS, Breitling R. Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries. Synth Biol (Oxf) 2019; 4:ysz025. [PMID: 32995546 PMCID: PMC7445882 DOI: 10.1093/synbio/ysz025] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 01/09/2023] Open
Abstract
Synthetic biology utilizes the Design-Build-Test-Learn pipeline for the engineering of biological systems. Typically, this requires the construction of specifically designed, large and complex DNA assemblies. The availability of cheap DNA synthesis and automation enables high-throughput assembly approaches, which generates a heavy demand for DNA sequencing to verify correctly assembled constructs. Next-generation sequencing is ideally positioned to perform this task, however with expensive hardware costs and bespoke data analysis requirements few laboratories utilize this technology in-house. Here a workflow for highly multiplexed sequencing is presented, capable of fast and accurate sequence verification of DNA assemblies using nanopore technology. A novel sample barcoding system using polymerase chain reaction is introduced, and sequencing data are analyzed through a bespoke analysis algorithm. Crucially, this algorithm overcomes the problem of high-error rate nanopore data (which typically prevents identification of single nucleotide variants) through statistical analysis of strand bias, permitting accurate sequence analysis with single-base resolution. As an example, 576 constructs (6 × 96 well plates) were processed in a single workflow in 72 h (from Escherichia coli colonies to analyzed data). Given our procedure's low hardware costs and highly multiplexed capability, this provides cost-effective access to powerful DNA sequencing for any laboratory, with applications beyond synthetic biology including directed evolution, single nucleotide polymorphism analysis and gene synthesis.
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Affiliation(s)
- Andrew Currin
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Neil Swainston
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK.,Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mark S Dunstan
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Adrian J Jervis
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Paul Mulherin
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Christopher J Robinson
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Sandra Taylor
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Pablo Carbonell
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Katherine A Hollywood
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Cunyu Yan
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Nigel S Scrutton
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.,School of Natural Sciences, Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
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32
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Klein CA, Emde L, Kuijpers A, Sobetzko P. MoCloFlex: A Modular Yet Flexible Cloning System. Front Bioeng Biotechnol 2019; 7:271. [PMID: 31750294 PMCID: PMC6843054 DOI: 10.3389/fbioe.2019.00271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/30/2019] [Indexed: 02/04/2023] Open
Abstract
Modern cloning solutions are gradually replacing classical cloning methods. Current systems make use of libraries with predefined DNA parts that are joined by Golden-Gate reactions. However, these systems still suffer from specific inflexibilities and the lack of inter-compatibility. Here, we present Flexible Modular Cloning (MoCloFlex) which overcomes this inflexibility by introducing a set of linker- and position-vectors allowing free unit arrangement. Our system, therefore, provides a convenient way to design and build custom plasmids, and iterative assembly of large constructs. To support standardization in synthetic biology, MoCloFlex is compatible with the well-established Modular Cloning standard. Here, we present and characterize MoCloFlex for various applications with up to 12 fragments in a single restriction-ligation reaction.
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Affiliation(s)
- Carlo A. Klein
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Leonie Emde
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Aaron Kuijpers
- Department of Biology, University of Kassel, Kassel, Germany
| | - Patrick Sobetzko
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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33
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Xia Y, Li K, Li J, Wang T, Gu L, Xun L. T5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis. Nucleic Acids Res 2019; 47:e15. [PMID: 30462336 PMCID: PMC6379645 DOI: 10.1093/nar/gky1169] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/31/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
The assembly of DNA fragments with homologous arms is becoming popular in routine cloning. For an in vitro assembly reaction, a DNA polymerase is often used either alone for its 3'-5' exonuclease activity or together with a 5'-3' exonuclease for its DNA polymerase activity. Here, we present a 'T5 exonuclease DNA assembly' (TEDA) method that only uses a 5'-3' exonuclease. DNA fragments with short homologous ends were treated by T5 exonuclease and then transformed into Escherichia coli to produce clone colonies. The cloning efficiency was similar to that of the commercial In-Fusion method employing a proprietary DNA polymerase, but higher than that of the Gibson method utilizing T5 exonuclease, Phusion DNA polymerase, and DNA ligase. It also assembled multiple DNA fragments and did simultaneous site-directed mutagenesis at multiple sites. The reaction mixture was simple, and each reaction used 0.04 U of T5 exonuclease that cost 0.25 US cents. The simplicity, cost effectiveness, and cloning efficiency should promote its routine use, especially for labs with a budget constraint. TEDA may trigger further development of DNA assembly methods that employ single exonucleases.
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Affiliation(s)
- Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Kai Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Jingjing Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Tianqi Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China.,School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
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34
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Nora LC, Westmann CA, Guazzaroni ME, Siddaiah C, Gupta VK, Silva-Rocha R. Recent advances in plasmid-based tools for establishing novel microbial chassis. Biotechnol Adv 2019; 37:107433. [PMID: 31437573 DOI: 10.1016/j.biotechadv.2019.107433] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 07/11/2019] [Accepted: 08/16/2019] [Indexed: 12/28/2022]
Abstract
A key challenge for domesticating alternative cultivable microorganisms with biotechnological potential lies in the development of innovative technologies. Within this framework, a myriad of genetic tools has flourished, allowing the design and manipulation of complex synthetic circuits and genomes to become the general rule in many laboratories rather than the exception. More recently, with the development of novel technologies such as DNA automated synthesis/sequencing and powerful computational tools, molecular biology has entered the synthetic biology era. In the beginning, most of these technologies were established in traditional microbial models (known as chassis in the synthetic biology framework) such as Escherichia coli and Saccharomyces cerevisiae, enabling fast advances in the field and the validation of fundamental proofs of concept. However, it soon became clear that these organisms, although extremely useful for prototyping many genetic tools, were not ideal for a wide range of biotechnological tasks due to intrinsic limitations in their molecular/physiological properties. Over the last decade, researchers have been facing the great challenge of shifting from these model systems to non-conventional chassis with endogenous capacities for dealing with specific tasks. The key to address these issues includes the generation of narrow and broad host plasmid-based molecular tools and the development of novel methods for engineering genomes through homologous recombination systems, CRISPR/Cas9 and other alternative methods. Here, we address the most recent advances in plasmid-based tools for the construction of novel cell factories, including a guide for helping with "build-your-own" microbial host.
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Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | | | - Vijai Kumar Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil.
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35
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Finnigan W, Cutlan R, Snajdrova R, Adams JP, Littlechild JA, Harmer NJ. Engineering a Seven Enzyme Biotransformation using Mathematical Modelling and Characterized Enzyme Parts. ChemCatChem 2019; 11:3474-3489. [PMID: 31598184 PMCID: PMC6774274 DOI: 10.1002/cctc.201900646] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/30/2019] [Indexed: 12/28/2022]
Abstract
Multi-step enzyme reactions offer considerable cost and productivity benefits. Process models offer a route to understanding the complexity of these reactions, and allow for their optimization. Despite the increasing prevalence of multi-step biotransformations, there are few examples of process models for enzyme reactions. From a toolbox of characterized enzyme parts, we demonstrate the construction of a process model for a seven enzyme, three step biotransformation using isolated enzymes. Enzymes for cofactor regeneration were employed to make this in vitro reaction economical. Good modelling practice was critical in evaluating the impact of approximations and experimental error. We show that the use and validation of process models was instrumental in realizing and removing process bottlenecks, identifying divergent behavior, and for the optimization of the entire reaction using a genetic algorithm. We validated the optimized reaction to demonstrate that complex multi-step reactions with cofactor recycling involving at least seven enzymes can be reliably modelled and optimized.
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Affiliation(s)
- William Finnigan
- Department of BiosciencesUniversity of Exeter Henry Wellcome Building for BiocatalysisStocker RoadExeterEX4 4QDUK
| | - Rhys Cutlan
- Living Systems InstituteUniversity of ExeterStocker RoadExeterEX4 4QDmUK
| | - Radka Snajdrova
- GlaxoSmithKline R&D LtdMedicines Research Centre Gunnels Wood Road, StevenageHertfordshireSG1 2NYUK
| | - Joseph P. Adams
- GlaxoSmithKline R&D LtdMedicines Research Centre Gunnels Wood Road, StevenageHertfordshireSG1 2NYUK
| | - Jennifer A. Littlechild
- Department of BiosciencesUniversity of Exeter Henry Wellcome Building for BiocatalysisStocker RoadExeterEX4 4QDUK
| | - Nicholas J. Harmer
- Department of BiosciencesUniversity of Exeter Henry Wellcome Building for BiocatalysisStocker RoadExeterEX4 4QDUK
- Living Systems InstituteUniversity of ExeterStocker RoadExeterEX4 4QDmUK
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36
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Roehner N, Bartley B, Beal J, McLaughlin J, Pocock M, Zhang M, Zundel Z, Myers CJ. Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL). ACS Synth Biol 2019; 8:1519-1523. [PMID: 31260271 DOI: 10.1021/acssynbio.9b00092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As improvements in DNA synthesis technology and assembly methods make combinatorial assembly of genetic constructs increasingly accessible, methods for representing genetic constructs likewise need to improve to handle the exponential growth of combinatorial design space. To this end, we present a community accepted extension of the SBOL data standard that allows for the efficient and flexible encoding of combinatorial designs. This extension includes data structures for representing genetic designs with "variable" components that can be implemented by choosing one of many linked designs for existing genetic parts or constructs. We demonstrate the representational power of the SBOL combinatorial design extension through case studies on metabolic pathway design and genetic circuit design, and we report the expansion of the SBOLDesigner software tool to support users in creating and modifying combinatorial designs in SBOL.
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Affiliation(s)
- Nicholas Roehner
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Bryan Bartley
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | | | - Matthew Pocock
- Turing Ate My Hamster, Ltd., Tyne and Wear, NE27 0RT, UK
| | - Michael Zhang
- University of Utah, Salt Lake City, Utah 84112, United States
| | - Zach Zundel
- University of Utah, Salt Lake City, Utah 84112, United States
| | - Chris J. Myers
- University of Utah, Salt Lake City, Utah 84112, United States
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37
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Liu S, Xiao H, Zhang F, Lu Z, Zhang Y, Deng A, Li Z, Yang C, Wen T. A seamless and iterative DNA assembly method named PS-Brick and its assisted metabolic engineering for threonine and 1-propanol production. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:180. [PMID: 31338122 PMCID: PMC6628500 DOI: 10.1186/s13068-019-1520-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND DNA assembly is an essential technique enabling metabolic engineering and synthetic biology. Combining novel DNA assembly technologies with rational metabolic engineering can facilitate the construction of microbial cell factories. Amino acids and derived biochemicals are important products in industrial biotechnology with wide application and huge markets. DNA assembly scenarios encountered in metabolic engineering for the construction of amino acid and related compound producers, such as design-build-test-learn cycles, construction of precise genetic circuits and repetitive DNA molecules, usually require for iterative, scarless and repetitive sequence assembly methods, respectively. RESULTS Restriction endonuclease (RE)-assisted strategies constitute one of the major categories of DNA assembly. Here, we developed a Type IIP and IIS RE-assisted method named PS-Brick that comprehensively takes advantage of the properties of PCR fragments and REs for iterative, seamless and repetitive sequence assembly. One round of PS-Brick reaction using purified plasmids and PCR fragments was accomplished within several hours, and transformation of the resultant reaction product from this PS-Brick assembly reaction exhibited high efficiency (104-105 CFUs/µg DNA) and high accuracy (~ 90%). An application of metabolic engineering to threonine production, including the release of feedback regulation, elimination of metabolic bottlenecks, intensification of threonine export and inactivation of threonine catabolism, was stepwise resolved in E. coli by rounds of "design-build-test-learn" cycles through the iterative PS-Brick paradigm, and 45.71 g/L threonine was obtained through fed-batch fermentation. In addition to the value of the iterative character of PS-Brick for sequential strain engineering, seamless cloning enabled precise in-frame fusion for codon saturation mutagenesis and bicistronic design, and the repetitive sequence cloning ability of PS-Brick enabled construction of tandem CRISPR sgRNA arrays for genome editing. Moreover, the heterologous pathway deriving 1-propanol pathway from threonine, composed of Lactococcus lactis kivD and Saccharomyces cerevisiae ADH2, was assembled by one cycle of PS-Brick, resulting in 1.35 g/L 1-propanol in fed-batch fermentation. CONCLUSIONS To the best of our knowledge, the PS-Brick framework is the first RE-assisted DNA assembly method using the strengths of both Type IIP and IIS REs. In this study, PS-Brick was demonstrated to be an efficient DNA assembly method for pathway construction and genome editing and was successfully applied in design-build-test-learn (DBTL) cycles of metabolic engineering for the production of threonine and threonine-derived 1-propanol. The PS-Brick presents a valuable addition to the current toolbox of synthetic biology and metabolic engineering.
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Affiliation(s)
- Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Haihan Xiao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fangfang Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, 230039 China
| | - Zheng Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Aihua Deng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhongcai Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Cui Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049 China
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38
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Walsh DI, Pavan M, Ortiz L, Wick S, Bobrow J, Guido NJ, Leinicke S, Fu D, Pandit S, Qin L, Carr PA, Densmore D. Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots. SLAS Technol 2019; 24:282-290. [PMID: 30768372 PMCID: PMC6819997 DOI: 10.1177/2472630318825335] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The advancement of synthetic biology requires the ability to create new DNA sequences to produce unique behaviors in biological systems. Automation is increasingly employed to carry out well-established assembly methods of DNA fragments in a multiplexed, high-throughput fashion, allowing many different configurations to be tested simultaneously. However, metrics are required to determine when automation is warranted based on factors such as assembly methodology, protocol details, and number of samples. The goal of our synthetic biology automation work is to develop and test protocols, hardware, and software to investigate and optimize DNA assembly through quantifiable metrics. We performed a parameter analysis of DNA assembly to develop a standardized, highly efficient, and reproducible MoClo protocol, suitable to be used both manually and with liquid-handling robots. We created a key DNA assembly metric (Q-metric) to characterize a given automation method's advantages over conventional manual manipulations with regard to researchers' highest-priority parameters: output, cost, and time. A software tool called Puppeteer was developed to formally capture these metrics, help define the assembly design, and provide human and robotic liquid-handling instructions. Altogether, we contribute to a growing foundation of standardizing practices, metrics, and protocols for automating DNA assembly.
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Affiliation(s)
- David I. Walsh
- Bioengineering Systems and Technologies, MIT-Lincoln Laboratory, Lexington, MA, USA
- Synthetic Biology Center at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marilene Pavan
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Luis Ortiz
- Biological Design Center, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry, Boston University, Boston, MA, USA
| | - Scott Wick
- Bioengineering Systems and Technologies, MIT-Lincoln Laboratory, Lexington, MA, USA
- Synthetic Biology Center at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Johanna Bobrow
- Bioengineering Systems and Technologies, MIT-Lincoln Laboratory, Lexington, MA, USA
- Synthetic Biology Center at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas J. Guido
- Bioengineering Systems and Technologies, MIT-Lincoln Laboratory, Lexington, MA, USA
- Synthetic Biology Center at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sarah Leinicke
- Hariri Institute for Computing, Boston University, Boston, MA, USA
| | - Dany Fu
- Hariri Institute for Computing, Boston University, Boston, MA, USA
| | - Shreya Pandit
- Hariri Institute for Computing, Boston University, Boston, MA, USA
| | - Lucy Qin
- Hariri Institute for Computing, Boston University, Boston, MA, USA
| | - Peter A. Carr
- Bioengineering Systems and Technologies, MIT-Lincoln Laboratory, Lexington, MA, USA
- Synthetic Biology Center at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Douglas Densmore
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
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39
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Engineering a minimal cloning vector from a pUC18 plasmid backbone with an extended multiple cloning site. Biotechniques 2019; 66:254-259. [DOI: 10.2144/btn-2019-0014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Minimal plasmids play an essential role in many intermediate steps in molecular biology. For example, they can be used to assemble building blocks in synthetic biology or be used as intermediate cloning plasmids that are ideal for PCR-based mutagenesis methods. A small backbone also opens up for additional unique restriction enzyme cloning sites. Here we describe the generation of pICOz, a 1185-bp fully functional high-copy cloning plasmid with an extended multiple cloning site. We believe that this is the smallest high-copy cloning vector ever described.
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40
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Li M, Li X, Chen X, Chen J. De novo synthesis of the complete genome of coxsackievirus A10 based on Golden Gate cloning combined with promoter reconstruction. Plasmid 2019; 103:17-24. [PMID: 30928703 DOI: 10.1016/j.plasmid.2019.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/09/2019] [Accepted: 03/09/2019] [Indexed: 11/22/2022]
Abstract
In the present study, a donor plasmid derived from pUC19 and two recipient plasmids, which had been modified from the donor plasmid and contained the red fluorescence protein gene mCherry as a reporter gene downstream of the hybrid tac promoter with the -35 region deletion mutation, were constructed. The complete genome sequence of coxsackievirus A10 downstream of the T7 promoter was divided into 7 fragments and synthesized by overlap extension PCR and the DNAworks program. Using the Golden Gate cloning strategy, the 7 fragments were then cloned into the donor plasmid and transferred to the recipient plasmid upstream of the deletion mutation tac promoter in a defined order and orientation without any deletions or insertions at the junction sites. Because the -35 region of the tac promoter was introduced into the 3' end of the last fragment during construction, the hybrid promoter was reconstructed to promote expression of mCherry, which facilitated the selection of colonies with the complete genome of coxsackievirus A10 to generate an infectious cDNA clone via reverse genetic engineering.
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Affiliation(s)
- Meng Li
- China National Biotech Group, Wuhan Institute of Biological Products Co., Ltd., Wuhan, People's Republic of China.
| | - Xinguo Li
- China National Biotech Group, Wuhan Institute of Biological Products Co., Ltd., Wuhan, People's Republic of China
| | - Xiaoqi Chen
- China National Biotech Group, Wuhan Institute of Biological Products Co., Ltd., Wuhan, People's Republic of China
| | - Jing Chen
- China National Biotech Group, Wuhan Institute of Biological Products Co., Ltd., Wuhan, People's Republic of China
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41
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Fedorec AJH, Ozdemir T, Doshi A, Ho YK, Rosa L, Rutter J, Velazquez O, Pinheiro VB, Danino T, Barnes CP. Two New Plasmid Post-segregational Killing Mechanisms for the Implementation of Synthetic Gene Networks in Escherichia coli. iScience 2019; 14:323-334. [PMID: 30954530 PMCID: PMC6489366 DOI: 10.1016/j.isci.2019.03.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/29/2018] [Accepted: 03/18/2019] [Indexed: 11/03/2022] Open
Abstract
Plasmids are the workhorse of both industrial biotechnology and synthetic biology, but ensuring they remain in bacterial cells is a challenge. Antibiotic selection cannot be used to stabilize plasmids in most real-world applications, and inserting dynamical gene networks into the genome remains challenging. Plasmids have evolved several mechanisms for stability, one of which, post-segregational killing (PSK), ensures that plasmid-free cells do not survive. Here we demonstrate the plasmid-stabilizing capabilities of the axe/txe toxin-antitoxin system and the microcin-V bacteriocin system in the probiotic bacteria Escherichia coli Nissle 1917 and show that they can outperform the commonly used hok/sok. Using plasmid stability assays, automated flow cytometry analysis, mathematical models, and Bayesian statistics we quantified plasmid stability in vitro. Furthermore, we used an in vivo mouse cancer model to demonstrate plasmid stability in a real-world therapeutic setting. These new PSK systems, plus the developed Bayesian methodology, will have wide applicability in clinical and industrial biotechnology.
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Affiliation(s)
- Alex J H Fedorec
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK; Centre for Mathematics, Physics and Engineering in the Life Sciences and Experimental Biology, University College London, London WC1E 6BT, UK.
| | - Tanel Ozdemir
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Anjali Doshi
- Department of Biomedical Engineering, Columbia University, New York City, NY 10027, USA
| | - Yan-Kay Ho
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Luca Rosa
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Jack Rutter
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Oscar Velazquez
- Department of Biomedical Engineering, Columbia University, New York City, NY 10027, USA
| | - Vitor B Pinheiro
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; KU Leuven Rega Institute for Medical Research, Herestraat, 49 Box 1030, 3000 Leuven, Belgium
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York City, NY 10027, USA; Data Science Institute, Columbia University, New York, NY 10027, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK; Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
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42
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Microfluidics for cell factory and bioprocess development. Curr Opin Biotechnol 2019; 55:95-102. [DOI: 10.1016/j.copbio.2018.08.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/24/2018] [Accepted: 08/31/2018] [Indexed: 12/18/2022]
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43
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McCarty NS, Ledesma-Amaro R. Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology. Trends Biotechnol 2019; 37:181-197. [PMID: 30497870 PMCID: PMC6340809 DOI: 10.1016/j.tibtech.2018.11.002] [Citation(s) in RCA: 225] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022]
Abstract
Microbial consortia have been used in biotechnology processes, including fermentation, waste treatment, and agriculture, for millennia. Today, synthetic biologists are increasingly engineering microbial consortia for diverse applications, including the bioproduction of medicines, biofuels, and biomaterials from inexpensive carbon sources. An improved understanding of natural microbial ecosystems, and the development of new tools to construct synthetic consortia and program their behaviors, will vastly expand the functions that can be performed by communities of interacting microorganisms. Here, we review recent advancements in synthetic biology tools and approaches to engineer synthetic microbial consortia, discuss ongoing and emerging efforts to apply consortia for various biotechnological applications, and suggest future applications.
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Affiliation(s)
- Nicholas S. McCarty
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
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44
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Gerasymenko I, Sheludko Y, Fräbel S, Staniek A, Warzecha H. Combinatorial biosynthesis of small molecules in plants: Engineering strategies and tools. Methods Enzymol 2019; 617:413-442. [PMID: 30784411 DOI: 10.1016/bs.mie.2018.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Biosynthetic capacity of plants, rooted in a near inexhaustible supply of photosynthetic energy and founded upon an intricate matrix of metabolic networks, makes them versatile chemists producing myriad specialized compounds. Along with tremendous success in elucidation of several plant biosynthetic routes, their reestablishment in heterologous hosts has been a hallmark of recent bioengineering endeavors. However, current efforts in the field are, in the main, aimed at grafting the pathways to fermentable recipient organisms, like bacteria or yeast. Conversely, while harboring orthologous metabolic trails, select plant species now emerge as viable vehicles for mobilization and engineering of complex biosynthetic pathways. Their distinctive features, like intricate cell compartmentalization and formation of specialized production and storage structures on tissue and organ level, make plants an especially promising chassis for the manufacture of considerable amounts of high-value natural small molecules. Inspired by the fundamental tenets of synthetic biology, capitalizing on the versatility of the transient plant transformation system, and drawing on the unique compartmentation of plant cells, we explore combinatorial approaches affording production of natural and new-to-nature, bespoke chemicals of potential importance. Here, we focus on the transient engineering of P450 monooxygenases, alone or in concert with other orthogonal catalysts, like tryptophan halogenases.
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Affiliation(s)
- Iryna Gerasymenko
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Darmstadt, Germany
| | - Yuriy Sheludko
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Darmstadt, Germany
| | - Sabine Fräbel
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Darmstadt, Germany
| | - Agata Staniek
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Darmstadt, Germany
| | - Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Darmstadt, Germany.
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45
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Nora LC, Westmann CA, Martins‐Santana L, Alves LDF, Monteiro LMO, Guazzaroni M, Silva‐Rocha R. The art of vector engineering: towards the construction of next-generation genetic tools. Microb Biotechnol 2019; 12:125-147. [PMID: 30259693 PMCID: PMC6302727 DOI: 10.1111/1751-7915.13318] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 12/20/2022] Open
Abstract
When recombinant DNA technology was developed more than 40 years ago, no one could have imagined the impact it would have on both society and the scientific community. In the field of genetic engineering, the most important tool developed was the plasmid vector. This technology has been continuously expanding and undergoing adaptations. Here, we provide a detailed view following the evolution of vectors built throughout the years destined to study microorganisms and their peculiarities, including those whose genomes can only be revealed through metagenomics. We remark how synthetic biology became a turning point in designing these genetic tools to create meaningful innovations. We have placed special focus on the tools for engineering bacteria and fungi (both yeast and filamentous fungi) and those available to construct metagenomic libraries. Based on this overview, future goals would include the development of modular vectors bearing standardized parts and orthogonally designed circuits, a task not fully addressed thus far. Finally, we present some challenges that should be overcome to enable the next generation of vector design and ways to address it.
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Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | | | - Luana de Fátima Alves
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
- School of Philosophy, Science and Letters of Ribeirão PretoUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | | | - María‐Eugenia Guazzaroni
- School of Philosophy, Science and Letters of Ribeirão PretoUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | - Rafael Silva‐Rocha
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
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46
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Mann DGJ, Bevan SA, Harvey AJ, Leffert-Sorenson RA. The Use of an Automated Platform to Assemble Multigenic Constructs for Plant Transformation. Methods Mol Biol 2019; 1864:19-35. [PMID: 30415326 DOI: 10.1007/978-1-4939-8778-8_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Compared to traditional means, modern DNA assembly methods allow cloning of large, multigenic vectors for plant transformation in rapid fashion. These methods are often robust and efficient and can assemble multiple DNA fragments into a single vector in one reaction. Here we describe the use of an automated DNA assembly platform for the generation of complex, multigenic T-DNA binary vectors using a hierarchical Golden Gate cloning strategy. These DNA constructs contained diverse DNA elements for the expression of multiple genes for trait stacking in the crop of interest. This platform streamlines the DNA assembly and validation process through high-efficiency cloning methods, integrated automation equipment, and increased throughput. The implementation of this platform removes bottlenecks for routine molecular biology and opens new possibilities for downstream experimental idea testing.
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Affiliation(s)
- David G J Mann
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA.
| | - Scott A Bevan
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA
| | - Anthony J Harvey
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA
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47
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Abstract
Synthetic biology has undergone dramatic advancements for over a decade, during which it has expanded our understanding on the systems of life and opened new avenues for microbial engineering. Many biotechnological and computational methods have been developed for the construction of synthetic systems. Achievements in synthetic biology have been widely adopted in metabolic engineering, a field aimed at engineering micro-organisms to produce substances of interest. However, the engineering of metabolic systems requires dynamic redistribution of cellular resources, the creation of novel metabolic pathways, and optimal regulation of the pathways to achieve higher production titers. Thus, the design principles and tools developed in synthetic biology have been employed to create novel and flexible metabolic pathways and to optimize metabolic fluxes to increase the cells’ capability to act as production factories. In this review, we introduce synthetic biology tools and their applications to microbial cell factory constructions.
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48
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Cassette hybridization for vector assembly application in antibody chain shuffling. Biotechniques 2018; 65:269-274. [DOI: 10.2144/btn-2018-0031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Gene assembly methods are an integral part of molecular cloning experiments. The majority of existing vector assembly methods stipulate a need for exonucleases, endonucleases and/or the use of single-stranded DNA as starting materials. Here, we introduced a vector assembly method that employs conventional PCR to amplify stable double-stranded DNA fragments and assembles them into functional vectors specifically for antibody chain shuffling. We successfully formed vectors using cassettes amplified from different templates and assembled an array of single chain fragment variable clones of fixed variable heavy chain, with different variable light chains – a chain shuffling process for antibody maturation. The method provides an easy alternative to the conventional cloning process.
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49
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Abstract
Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry—biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function.
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Affiliation(s)
- Caleb J. Bashor
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;,
| | - James J. Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;,
- Harvard–MIT Program in Health Sciences and Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
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50
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He Y, Wang B, Chen W, Cox RJ, He J, Chen F. Recent advances in reconstructing microbial secondary metabolites biosynthesis in Aspergillus spp. Biotechnol Adv 2018; 36:739-783. [DOI: 10.1016/j.biotechadv.2018.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 11/28/2022]
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