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Hernández-Rollán C, Ehrmann AK, Vlassis A, Kandasamy V, Nørholm MHH. Neq2X7: a multi-purpose and open-source fusion DNA polymerase for advanced DNA engineering and diagnostics PCR. BMC Biotechnol 2024; 24:17. [PMID: 38566117 PMCID: PMC10988834 DOI: 10.1186/s12896-024-00844-7] [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: 12/01/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Thermostable DNA polymerases, such as Taq isolated from the thermophilic bacterium Thermus aquaticus, enable one-pot exponential DNA amplification known as polymerase chain reaction (PCR). However, properties other than thermostability - such as fidelity, processivity, and compatibility with modified nucleotides - are important in contemporary molecular biology applications. Here, we describe the engineering and characterization of a fusion between a DNA polymerase identified in the marine archaea Nanoarchaeum equitans and a DNA binding domain from the thermophile Sulfolobus solfataricus. The fusion creates a highly active enzyme, Neq2X7, capable of amplifying long and GC-rich DNA, unaffected by replacing dTTP with dUTP in PCR, and tolerant to various known PCR inhibitors. This makes it an attractive DNA polymerase for use, e.g., with uracil excision (USER) DNA assembly and for contamination-free diagnostics. Using a magnification via nucleotide imbalance fidelity assay, Neq2X7 was estimated to have an error rate lower than 2 ∙ 10-5 bp-1 and an approximately 100x lower fidelity than the parental variant Neq2X, indicating a trade-off between fidelity and processivity - an observation that may be of importance for similarly engineered DNA polymerases. Neq2X7 is easy to produce for routine application in any molecular biology laboratory, and the expression plasmid is made freely available.
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Affiliation(s)
- Cristina Hernández-Rollán
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, Kongens Lyngby, 2800, Denmark
| | - Anja K Ehrmann
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, Kongens Lyngby, 2800, Denmark
| | - Arsenios Vlassis
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, Kongens Lyngby, 2800, Denmark
| | - Vijayalakshmi Kandasamy
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, Kongens Lyngby, 2800, Denmark
| | - Morten H H Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, Kongens Lyngby, 2800, Denmark.
- Mycropt ApS, Kongens Lyngby, 2800, Denmark.
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2
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Wang X, Li A, Li X, Cui H. Empowering Protein Engineering through Recombination of Beneficial Substitutions. Chemistry 2024; 30:e202303889. [PMID: 38288640 DOI: 10.1002/chem.202303889] [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: 01/04/2024] [Indexed: 02/24/2024]
Abstract
Directed evolution stands as a seminal technology for generating novel protein functionalities, a cornerstone in biocatalysis, metabolic engineering, and synthetic biology. Today, with the development of various mutagenesis methods and advanced analytical machines, the challenge of diversity generation and high-throughput screening platforms is largely solved, and one of the remaining challenges is: how to empower the potential of single beneficial substitutions with recombination to achieve the epistatic effect. This review overviews experimental and computer-assisted recombination methods in protein engineering campaigns. In addition, integrated and machine learning-guided strategies were highlighted to discuss how these recombination approaches contribute to generating the screening library with better diversity, coverage, and size. A decision tree was finally summarized to guide the further selection of proper recombination strategies in practice, which was beneficial for accelerating protein engineering.
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Affiliation(s)
- Xinyue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Haiyang Cui
- School of Life Sciences, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
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3
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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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4
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Vo-Nguyen HV, Nguyen TT, Mai QG, Tran TT, Tran TL, Tran-Van H. Recombinase-free cloning (RFC) protocol for gene swapping. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2022; 11:21-27. [PMID: 35463820 PMCID: PMC9012429 DOI: 10.22099/mbrc.2021.41923.1685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Recombinant DNA technology has been playing the key role for a long time since its first beginning. DNA ligases have certainly contributed to the development of cloning techniques, as well as molecular study up to now. Despite being a prime cloning tool, DNA ligases still face some shortcomings which lead to their limit of use. Our study provided an improved method that simplified the basic restriction enzyme-based cloning (REC) by eliminating the ligation role, named recombinase-free cloning (RFC). This improved technique was designed with only one PCR reaction, one digestion reaction, and one temperature profile, which takes advantage of endogenous recombinase in E. coli host to create the target recombinant vector inside the cell. All purification steps were eliminated for effectively material- and time-saving. Five different clones were generated by RFC. This method showed relatively low efficiency yet successful at a range of 100% in every conducted trial with fragment sizes from 0.5-1.0 kbp. The RFC method could be completed within a day (about 9 hours), without the need of ligase or recombinase or purification steps, which significantly saved DNA components, materials as well as the time required. In conclusion, we expected to provide a more convenient cloning method, as well as enable faster generation of DNA clones, which would be well applied in the less equipped laboratories.
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Affiliation(s)
- Hai-Vy Vo-Nguyen
- Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Laboratory of Biosensors, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thanh-Tan Nguyen
- Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Vietnam National University, Ho Chi Minh City, Vietnam
| | - Quoc-Gia Mai
- Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Laboratory of Biosensors, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thien-Thien Tran
- Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thuoc Linh Tran
- Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Laboratory of Biosensors, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Vietnam National University, Ho Chi Minh City, Vietnam
| | - Hieu Tran-Van
- Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Laboratory of Biosensors, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam,Vietnam National University, Ho Chi Minh City, Vietnam,Corresponding Author: Department Molecular and Environmental Biotechnology, Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, Vietnam, Tel: +8428 62884499; Fax: +8428 38350096. E. mail:
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5
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Liu Z, Wang J, Nielsen J. Yeast synthetic biology advances biofuel production. Curr Opin Microbiol 2021; 65:33-39. [PMID: 34739924 DOI: 10.1016/j.mib.2021.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 01/24/2023]
Abstract
Increasing concerns of environmental impacts and global warming calls for urgent need to switch from use of fossil fuels to renewable technologies. Biofuels represent attractive alternatives of fossil fuels and have gained continuous attentions. Through the use of synthetic biology it has become possible to engineer microbial cell factories for efficient biofuel production in a more precise and efficient manner. Here, we review advances on yeast-based biofuel production. Following an overview of synthetic biology impacts on biofuel production, we review recent advancements on the design, build, test, learn steps of yeast-based biofuel production, and end with discussion of challenges associated with use of synthetic biology for developing novel processes for biofuel production.
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Affiliation(s)
- Zihe Liu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Junyang Wang
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Jens Nielsen
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China; Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen N, Denmark.
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6
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Wang W, Zheng G, Lu Y. Recent Advances in Strategies for the Cloning of Natural Product Biosynthetic Gene Clusters. Front Bioeng Biotechnol 2021; 9:692797. [PMID: 34327194 PMCID: PMC8314000 DOI: 10.3389/fbioe.2021.692797] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/18/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial natural products (NPs) are a major source of pharmacological agents. Most NPs are synthesized from specific biosynthetic gene clusters (BGCs). With the rapid increase of sequenced microbial genomes, large numbers of NP BGCs have been discovered, regarded as a treasure trove of novel bioactive compounds. However, many NP BGCs are silent in native hosts under laboratory conditions. In order to explore their therapeutic potential, a main route is to activate these silent NP BGCs in heterologous hosts. To this end, the first step is to accurately and efficiently capture these BGCs. In the past decades, a large number of effective technologies for cloning NP BGCs have been established, which has greatly promoted drug discovery research. Herein, we describe recent advances in strategies for BGC cloning, with a focus on the preparation of high-molecular-weight DNA fragment, selection and optimization of vectors used for carrying large-size DNA, and methods for assembling targeted DNA fragment and appropriate vector. The future direction into novel, universal, and high-efficiency methods for cloning NP BGCs is also prospected.
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Affiliation(s)
- Wenfang Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guosong Zheng
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, China.,Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
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7
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Liu L, Chen Y, Yu S, Chen J, Zhou J. Simultaneous transformation of five vectors in Gluconobacter oxydans. Plasmid 2021; 117:102588. [PMID: 34256060 DOI: 10.1016/j.plasmid.2021.102588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 11/19/2022]
Abstract
Gluconobacter oxydans is an obligate Gram-negative bacterium that belongs to the family Acetobacteraceae. It is one of the most frequently used microorganisms in industrial biotechnology to produce chemicals related to incomplete oxidation. However, the fine-tuning of G. oxydans is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. Thus, a series of shuttle vectors for G. oxydans inspired by a series of wild-type plasmids in different G. oxydans strains were constructed. Fifteen shuttle vectors were employed to express mCherry in G. oxydans WSH-003 using the replication origin of these wild-type plasmids. Among them, the intensity of fluorescent proteins expressed by p15-K-mCherry was about 10 times that of fluorescent proteins expressed by p5-K-mCherry. Quantitative real-time polymerase chain reaction showed that the relative copy number of p15-K-mCherry reached 19 and had high stability. In contrast, some of the plasmids had a relative copy number of less than 10. The co-expression of multiple shuttle vectors revealed five shuttle vectors that could be transformed into G. oxydans WSH-003 and could express five different fluorescent proteins. The shuttle vectors will facilitate genetic operations for Gluconobacter strains to produce useful compounds more efficiently.
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Affiliation(s)
- Li Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yue Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shiqin Yu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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8
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Simple and efficient custom transcription activator-like effector gene synthesis via twin primer assembly. Biotechniques 2021; 70:100-106. [PMID: 33415991 DOI: 10.2144/btn-2020-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Transcription activator-like effector (TALE) nucleases (TALENs) efficiently recognize and cleave DNA in a sequence-dependent manner. However, current TALE custom synthesis methods are either complicated or expensive. Here we report a simple and low-cost method for TALE construct assembly. This method utilizes the denaturation/reannealing nature of double-stranded DNA to create a unique single-stranded DNA overhang for proper ordering of TALE monomers in an engineered multimer. We successfully synthesized two TALEN pairs targeting the endogenous TET1 locus in human embryonic kidney cells and demonstrated their editing efficiency. Our method provides an alternative simple, low-cost method for effective TALEN assembly, which may improve the application of TALE-based technology.
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9
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Young R, Haines M, Storch M, Freemont PS. Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly. Metab Eng 2020; 63:81-101. [PMID: 33301873 DOI: 10.1016/j.ymben.2020.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022]
Abstract
Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.
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Affiliation(s)
- Rosanna Young
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Matthew Haines
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Marko Storch
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK
| | - Paul S Freemont
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK; UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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10
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Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nat Commun 2020; 11:5294. [PMID: 33082347 PMCID: PMC7576135 DOI: 10.1038/s41467-020-19124-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022] Open
Abstract
Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host. Non-model bacteria offer unique and versatile metabolisms for synthetic biology. In this Perspective, the authors explore the limited availability of well-characterised biological parts in these species and argue that bacteriophages represent a diverse trove of orthogonal parts.
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11
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Yang H, Qin J, Wang X, EI-Shora HM, Yu B. Production of plant-derived anticancer precursor glucoraphanin in chromosomally engineered Escherichia coli. Microbiol Res 2020; 238:126484. [DOI: 10.1016/j.micres.2020.126484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/14/2020] [Accepted: 03/28/2020] [Indexed: 01/07/2023]
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12
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An artificial chromosome ylAC enables efficient assembly of multiple genes in Yarrowia lipolytica for biomanufacturing. Commun Biol 2020; 3:199. [PMID: 32350406 PMCID: PMC7190667 DOI: 10.1038/s42003-020-0936-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/07/2020] [Indexed: 12/18/2022] Open
Abstract
The efficient use of the yeast Yarrowia lipolytica as a cell factory is hampered by the lack of powerful genetic engineering tools dedicated for the assembly of large DNA fragments and the robust expression of multiple genes. Here we describe the design and construction of artificial chromosomes (ylAC) that allow easy and efficient assembly of genes and chromosomal elements. We show that metabolic pathways can be rapidly constructed by various assembly of multiple genes in vivo into a complete, independent and linear supplementary chromosome with a yield over 90%. Additionally, our results reveal that ylAC can be genetically maintained over multiple generations either under selective conditions or, without selective pressure, using an essential gene as the selection marker. Overall, the ylACs reported herein are game-changing technology for Y. lipolytica, opening myriad possibilities, including enzyme screening, genome studies and the use of this yeast as a previous unutilized bio-manufacturing platform. Zhong-peng Guo et al. develop artificial chromosomes (ylAC) that allow easy and efficient assembly of multiple genes in Yarrowia lipolytica, a yeast strain commonly used for synthetic biology. ylAC provides an improved bio-manufacturing platform that is potentially useful for food, pharmaceutical, and environmental industries.
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13
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Nawrath MM, Ottenheim C, Wu JC, Zimmermann W. Pantoea sp. P37 as a novel nonpathogenic host for the heterologous production of rhamnolipids. Microbiologyopen 2020; 9:e1019. [PMID: 32113194 PMCID: PMC7221421 DOI: 10.1002/mbo3.1019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/08/2020] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
Abstract
Microbially derived surfactants, so‐called biosurfactants, have attracted significant attention as an environmentally friendly alternative to their chemically synthesized counterparts. Particularly, rhamnolipids offer a large potential with their outstanding surfactant properties such as complete biodegradability, low toxicity, and stability. Rhamnolipids are naturally synthesized by the opportunistic human pathogen Pseudomonas aeruginosa under the tight regulation of a highly complex quorum‐sensing system. The heterologous production of mono‐rhamnolipids by a newly isolated nonpathogenic strain of the genus Pantoea was investigated. Analysis of the genome obtained by a chimeric assembly of Nanopore long reads and high‐quality Illumina reads suggested that the strain has evolved to an epiphytic rather than a pathogenic lifestyle. Functional heterologous expression of the mono‐rhamnolipid operon rhlAB derived from a P. aeruginosa strain was established and confirmed by HPLC analysis. Transcriptome analysis indicated destabilizing effects of the produced rhamnolipids on the cell envelope of the host resulting in the induction of molecular stress responses. After integration of the rmlBCDA operon, extracellular rhamnolipids in amounts up to 0.4 g/L could be detected and were identified as a mono‐rhamnolipid Rha‐C10‐C10 by MALDI‐TOF mass spectrometry.
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Affiliation(s)
- Margarete Monika Nawrath
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, Leipzig, Germany.,Institute of Chemical and Engineering Sciences, Agency for Sciences, Technology and Research (A*STAR), Singapore City, Singapore
| | - Christoph Ottenheim
- Institute of Chemical and Engineering Sciences, Agency for Sciences, Technology and Research (A*STAR), Singapore City, Singapore
| | - Jin Chuan Wu
- Institute of Chemical and Engineering Sciences, Agency for Sciences, Technology and Research (A*STAR), Singapore City, Singapore
| | - Wolfgang Zimmermann
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, Leipzig, Germany
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14
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Yan P, Zeng Y, Shen W, Tuo D, Li X, Zhou P. Nimble Cloning: A Simple, Versatile, and Efficient System for Standardized Molecular Cloning. Front Bioeng Biotechnol 2020; 7:460. [PMID: 32010678 PMCID: PMC6974442 DOI: 10.3389/fbioe.2019.00460] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
Molecular cloning is one of the most fundamental technologies in molecular biology, and has been critical for driving biotechnological advances. In this study, we have developed a novel method for standardized molecular cloning. The cloning technique known as "Nimble Cloning" uses the restriction enzyme, SfiI, in combination with the T5 exonuclease, to linearize the vector and generate 3'-overhangs simultaneously. Both PCR products and plasmids can be used for the cloning reaction in the Nimble Cloning system. The cloning system is highly efficient, suitable for gene expression in both prokaryotic and eukaryotic expression systems, and enables the reuse of DNA fragments or plasmid entry clones. Nimble Cloning is applicable for the cloning of single or multiple fragments, as well as multi-site cloning. Due also to its simplicity and versatility, the cloning method has great potential for the modular assembly of DNA constructs.
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Affiliation(s)
- Pu Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yanjing Zeng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Decai Tuo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiaoying Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Peng Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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15
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Programmed assembly of long DNA synthons: design, mechanism, and online monitoring. Appl Microbiol Biotechnol 2019; 103:9103-9117. [PMID: 31515595 DOI: 10.1007/s00253-019-10099-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/07/2019] [Accepted: 08/21/2019] [Indexed: 10/26/2022]
Abstract
Synthesis of custom de novo DNA sequences is highly demanded by fast-growing field of synthetic biology. Usually DNA sequences with length more than 1 kb are assembled from smaller synthetic DNA fragments (synthons) obtained by PCR assembly. The ability to synthesize longer synthons sufficiently reduces efforts and time for DNA synthesis. We developed a novel rational oligonucleotide design and programmed approach for the assembly of synthetic DNA synthons up to 1550 bp. The developed procedure was thoroughly investigated by synthesis of cholesterol oxidase gene from Streptomyces lavendulae (1544 bp). Our approach is based on combined design, oligonucleotide concentration gradient, and specialized assembly program that directs assembly reaction to full-length gene in a stepwise manner. The process includes conventional thermodynamically balanced assembly, thermodynamically balanced inside-out elongation, and further amplification. The ability of DNA polymerase to perform programmed assembly is highly influenced by the presence of 5' → 3'-exonuclease activity. Oligonucleotide probing of PCR assembly products allowed us to shed light on the nature of high molecular weight spurious by-products and to understand the mechanism of their formation. For the first time, we applied light scattering techniques for tracking of oligonucleotide annealing, analysis of gene assembly products, and even for real-time monitoring of gene assembly process.
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Zhang JJ, Tang X, Moore BS. Genetic platforms for heterologous expression of microbial natural products. Nat Prod Rep 2019; 36:1313-1332. [PMID: 31197291 PMCID: PMC6750982 DOI: 10.1039/c9np00025a] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Covering: 2005 up to 2019Natural products are of paramount importance in human medicine. Not only are most antibacterial and anticancer drugs derived directly from or inspired by natural products, many other branches of medicine, such as immunology, neurology, and cardiology, have similarly benefited from natural product-based drugs. Typically, the genetic material required to synthesize a microbial specialized product is arranged in a multigene biosynthetic gene cluster (BGC), which codes for proteins associated with molecule construction, regulation, and transport. The ability to connect natural product compounds to BGCs and vice versa, along with ever-increasing knowledge of biosynthetic machineries, has spawned the field of genomics-guided natural product genome mining for the rational discovery of new chemical entities. One significant challenge in the field of natural product genome mining is how to rapidly link orphan biosynthetic genes to their associated chemical products. This review highlights state-of-the-art genetic platforms to identify, interrogate, and engineer BGCs from diverse microbial sources, which can be broken into three stages: (1) cloning and isolation of genomic loci, (2) heterologous expression in a host organism, and (3) genetic manipulation of cloned pathways. In the future, we envision natural product genome mining will be rapidly accelerated by de novo DNA synthesis and refactoring of whole biosynthetic pathways in combination with systematic heterologous expression methodologies.
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Affiliation(s)
- Jia Jia Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Xiaoyu Tang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
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17
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Taylor GM, Mordaka PM, Heap JT. Start-Stop Assembly: a functionally scarless DNA assembly system optimized for metabolic engineering. Nucleic Acids Res 2019; 47:e17. [PMID: 30462270 PMCID: PMC6379671 DOI: 10.1093/nar/gky1182] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022] Open
Abstract
DNA assembly allows individual DNA constructs or libraries to be assembled quickly and reliably. Most methods are either: (i) Modular, easily scalable and suitable for combinatorial assembly, but leave undesirable 'scar' sequences; or (ii) bespoke (non-modular), scarless but less suitable for construction of combinatorial libraries. Both have limitations for metabolic engineering. To overcome this trade-off we devised Start-Stop Assembly, a multi-part, modular DNA assembly method which is both functionally scarless and suitable for combinatorial assembly. Crucially, 3 bp overhangs corresponding to start and stop codons are used to assemble coding sequences into expression units, avoiding scars at sensitive coding sequence boundaries. Building on this concept, a complete DNA assembly framework was designed and implemented, allowing assembly of up to 15 genes from up to 60 parts (or mixtures); monocistronic, operon-based or hybrid configurations; and a new streamlined assembly hierarchy minimizing the number of vectors. Only one destination vector is required per organism, reflecting our optimization of the system for metabolic engineering in diverse organisms. Metabolic engineering using Start-Stop Assembly was demonstrated by combinatorial assembly of carotenoid pathways in Escherichia coli resulting in a wide range of carotenoid production and colony size phenotypes indicating the intended exploration of design space.
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Affiliation(s)
- George M Taylor
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Paweł M Mordaka
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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18
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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: 142] [Impact Index Per Article: 28.4] [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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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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20
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Naseri G, Behrend J, Rieper L, Mueller-Roeber B. COMPASS for rapid combinatorial optimization of biochemical pathways based on artificial transcription factors. Nat Commun 2019; 10:2615. [PMID: 31197154 PMCID: PMC6565718 DOI: 10.1038/s41467-019-10224-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/26/2019] [Indexed: 02/08/2023] Open
Abstract
Balanced expression of multiple genes is central for establishing new biosynthetic pathways or multiprotein cellular complexes. Methods for efficient combinatorial assembly of regulatory sequences (promoters) and protein coding sequences are therefore highly wanted. Here, we report a high-throughput cloning method, called COMPASS for COMbinatorial Pathway ASSembly, for the balanced expression of multiple genes in Saccharomyces cerevisiae. COMPASS employs orthogonal, plant-derived artificial transcription factors (ATFs) and homologous recombination-based cloning for the generation of thousands of individual DNA constructs in parallel. The method relies on a positive selection of correctly assembled pathway variants from both, in vivo and in vitro cloning procedures. To decrease the turnaround time in genomic engineering, COMPASS is equipped with multi-locus CRISPR/Cas9-mediated modification capacity. We demonstrate the application of COMPASS by generating cell libraries producing β-carotene and co-producing β-ionone and biosensor-responsive naringenin. COMPASS will have many applications in synthetic biology projects that require gene expression balancing. Metabolic engineering requires the balancing of gene expression to obtain optimal output. Here the authors present COMPASS – COMbinatorial Pathway ASSembly – which uses plant-derived artificial transcription factors and cloning of thousands of DNA constructs in parallel to rapidly optimise pathways.
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Affiliation(s)
- Gita Naseri
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,University of Potsdam, Department Molecular Biology, Karl-Liebknecht-Str. 24-25, House 20, 14476, Potsdam, Germany
| | - Jessica Behrend
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Lisa Rieper
- University of Potsdam, Cell2Fab Research Unit, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Bernd Mueller-Roeber
- University of Potsdam, Department Molecular Biology, Karl-Liebknecht-Str. 24-25, House 20, 14476, Potsdam, Germany. .,Max-Planck Institute of Molecular Plant Physiology, Plant Signalling Group, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany. .,Center of Plant Systems Biology and Biotechnology (CPSBB), Department Plant Development, Ruski Blvd. 139, 4000, Plovdiv, Bulgaria.
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21
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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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22
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HamediRad M, Weisberg S, Chao R, Lian J, Zhao H. Highly Efficient Single-Pot Scarless Golden Gate Assembly. ACS Synth Biol 2019; 8:1047-1054. [PMID: 31013062 DOI: 10.1021/acssynbio.8b00480] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Golden Gate assembly is one of the most widely used DNA assembly methods due to its robustness and modularity. However, despite its popularity, the need for BsaI-free parts, the introduction of scars between junctions, as well as the lack of a comprehensive study on the linkers hinders its more widespread use. Here, we first developed a novel sequencing scheme to test the efficiency and specificity of 96 linkers of 4-bp length and experimentally verified these linkers and their effects on Golden Gate assembly efficiency and specificity. We then used this sequencing data to generate 200 distinct linker sets that can be used by the community to perform efficient Golden Gate assemblies of different sizes and complexity. We also present a single-pot scarless Golden Gate assembly and BsaI removal scheme and its accompanying assembly design software to perform point mutations and Golden Gate assembly. This assembly scheme enables scarless assembly without compromising efficiency by choosing optimized linkers near assembly junctions.
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Affiliation(s)
| | | | | | | | - Huimin Zhao
- Departments of Chemistry and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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23
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Metagenomics Approaches in Discovery and Development of New Bioactive Compounds from Marine Actinomycetes. Curr Microbiol 2019; 77:645-656. [PMID: 31069462 DOI: 10.1007/s00284-019-01698-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/26/2019] [Indexed: 02/06/2023]
Abstract
Marine actinomycetes are prolific sources of marine drug discovery system contributing for several bioactive compounds of biomedical prominence. Metagenomics, a culture-independent technique through its sequence- and function-based screening has led to the discovery and synthesis of numerous biologically significant compounds like polyketide synthase, Non-ribosomal peptide synthetase, antibiotics, and biocatalyst. While metagenomics offers different advantages over conventional sequencing techniques, they also have certain limitations including bias classification, non-availability of quality DNA samples, heterologous expression, and host selection. The assimilation of advanced amplification and screening methods such as φ29 DNA polymerase, Next-Generation Sequencing, Cosmids, and recent bioinformatics tools like automated genome mining, anti-SMASH have shown promising results to overcome these constrains. Consequently, functional genomics and bioinformatics along with synthetic biology will be crucial for the success of the metagenomic approach and indeed for exploring new possibilities among the microbial consortia for the future drug discovery process.
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Direct cloning and heterologous expression of natural product biosynthetic gene clusters by transformation-associated recombination. Methods Enzymol 2019; 621:87-110. [PMID: 31128791 DOI: 10.1016/bs.mie.2019.02.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Heterologous expression of natural product biosynthetic gene clusters (BGCs) is a robust approach not only to decipher biosynthetic logic behind natural product (NP) biosynthesis, but also to discover new chemicals from uncharacterized BGCs. This approach largely relies on techniques used for cloning large BGCs into suitable expression vectors. Recently, several whole-pathway direct cloning approaches, including full-length RecE-mediated recombination in Escherichia coli, Cas9-assisted in vitro assembly, and transformation-associated recombination (TAR) in Saccharomyces cerevisiae, have been developed to accelerate BGC isolation. In this chapter, we summarize a protocol for TAR cloning large NP BGCs, detailing the process of choosing TAR plasmids, designing pathway-specific TAR vectors, generating yeast spheroplasts, performing yeast transformation, and heterologously expressing BGCs in various host strains. We believe that the established platforms can accelerate the process of discovering new NPs, understanding NP biosynthetic logic, and engineering biosynthetic pathways.
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25
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Li WY, Liu CJ, Wu L, Wu JF, Yin XN, Deng KH, Zhang DY, Meng E. MCT cloning: a seamless cloning strategy for inserting DNA fragments. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1507756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Wen-Ying Li
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Chang-Jun Liu
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Lei Wu
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Jin-Feng Wu
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Xi-Nong Yin
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Kai-Hang Deng
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Dong-Yi Zhang
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
| | - Er Meng
- Research Center of Biological Information, College of Science, National University of Defense Technology, Changsha, Hunan, PR China
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26
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Yan F, Burgard C, Popoff A, Zaburannyi N, Zipf G, Maier J, Bernauer HS, Wenzel SC, Müller R. Synthetic biology approaches and combinatorial biosynthesis towards heterologous lipopeptide production. Chem Sci 2018; 9:7510-7519. [PMID: 30319751 PMCID: PMC6180311 DOI: 10.1039/c8sc02046a] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/08/2018] [Indexed: 12/14/2022] Open
Abstract
Synthetic biology techniques coupled with heterologous secondary metabolite production offer opportunities for the discovery and optimisation of natural products.
Synthetic biology techniques coupled with heterologous secondary metabolite production offer opportunities for the discovery and optimisation of natural products. Here we developed a new assembly strategy based on type IIS endonucleases and elaborate synthetic DNA platforms, which could be used to seamlessly assemble and engineer biosynthetic gene clusters (BGCs). By applying this versatile tool, we designed and assembled more than thirty different artificial myxochromide BGCs, each around 30 kb in size, and established heterologous expression platforms using a derivative of Myxococcus xanthus DK1622 as a host. In addition to the five native types of myxochromides (A, B, C, D and S), novel lipopeptide structures were produced by combinatorial exchange of nonribosomal peptide synthetase (NRPS) encoding genes from different myxochromide BGCs. Inspired by the evolutionary diversification of the native myxochromide megasynthetases, the ancestral A-type NRPS was engineered by inactivation, deletion, or duplication of catalytic domains and successfully converted into functional B-, C- and D-type megasynthetases. The constructional design approach applied in this study enables combinatorial engineering of complex synthetic BGCs and has great potential for the exploitation of other natural product biosynthetic pathways.
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Affiliation(s)
- Fu Yan
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Christian Burgard
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Alexander Popoff
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Nestor Zaburannyi
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Gregor Zipf
- ATG:biosynthetics GmbH , Weberstraße 40 , 79249 Merzhausen , Germany
| | - Josef Maier
- IStLS - Information Services to Life Sciences , Härlestraße 24/1 , 78727 Oberndorf am Neckar/Boll , Germany
| | - Hubert S Bernauer
- ATG:biosynthetics GmbH , Weberstraße 40 , 79249 Merzhausen , Germany
| | - Silke C Wenzel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research and Department of Pharmacy at Saarland University , Saarland University Campus , Building E8.1 , 66123 Saarbrücken , Germany .
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27
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Katz L, Chen YY, Gonzalez R, Peterson TC, Zhao H, Baltz RH. Synthetic biology advances and applications in the biotechnology industry: a perspective. ACTA ACUST UNITED AC 2018; 45:449-461. [DOI: 10.1007/s10295-018-2056-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/06/2018] [Indexed: 12/22/2022]
Abstract
Abstract
Synthetic biology is a logical extension of what has been called recombinant DNA (rDNA) technology or genetic engineering since the 1970s. As rDNA technology has been the driver for the development of a thriving biotechnology industry today, starting with the commercialization of biosynthetic human insulin in the early 1980s, synthetic biology has the potential to take the industry to new heights in the coming years. Synthetic biology advances have been driven by dramatic cost reductions in DNA sequencing and DNA synthesis; by the development of sophisticated tools for genome editing, such as CRISPR/Cas9; and by advances in informatics, computational tools, and infrastructure to facilitate and scale analysis and design. Synthetic biology approaches have already been applied to the metabolic engineering of microorganisms for the production of industrially important chemicals and for the engineering of human cells to treat medical disorders. It also shows great promise to accelerate the discovery and development of novel secondary metabolites from microorganisms through traditional, engineered, and combinatorial biosynthesis. We anticipate that synthetic biology will continue to have broadening impacts on the biotechnology industry to address ongoing issues of human health, world food supply, renewable energy, and industrial chemicals and enzymes.
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Affiliation(s)
- Leonard Katz
- 0000 0001 2181 7878 grid.47840.3f QB3 Institute University of California-Berkeley 5885 Hollis St., 4th Floor 94608 Emeryville CA USA
| | - Yvonne Y Chen
- 0000 0000 9632 6718 grid.19006.3e Department of Chemical and Biomolecular Engineering University of California-Los Angeles 420 Westwood Plaza, Boelter Hall 5531 90095 Los Angeles CA USA
| | - Ramon Gonzalez
- 0000 0004 1936 8278 grid.21940.3e Departments of Chemical and Biomolecular Engineering and Bioengineering Rice University 6100 Main Street 77005 Houston TX USA
| | - Todd C Peterson
- grid.427368.c Synthetic Genomics, Inc. 11149 North Torrey Pines Road 92037 La Jolla CA USA
| | - Huimin Zhao
- 0000 0004 1936 9991 grid.35403.31 Department of Chemical and Biomolecular Engineering University of Illinois 600 South Mathews Avenue 61801 Urbana IL USA
| | - Richard H Baltz
- CognoGen Biotechnology Consulting 7636 Andora Drive 34238 Sarasota FL USA
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Eyles TH, Vior NM, Truman AW. Rapid and Robust Yeast-Mediated Pathway Refactoring Generates Multiple New Bottromycin-Related Metabolites. ACS Synth Biol 2018; 7:1211-1218. [PMID: 29694038 DOI: 10.1021/acssynbio.8b00038] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Heterologous expression of biosynthetic gene clusters (BGCs) represents an attractive route to the production of new natural products, but is often hampered by poor yields. It is therefore important to develop tools that enable rapid refactoring, gene insertion/deletion, and targeted mutations in BGCs. Ideally, these tools should be highly efficient, affordable, accessible, marker free, and flexible for use with a wide range of BGCs. Here, we present a one-step yeast-based method that enables efficient, cheap, and flexible modifications to BGCs. Using the BGC for the antibiotic bottromycin, we showcase multiple modifications including refactoring, gene deletions and targeted mutations. This facilitated the construction of an inducible, riboswitch-controlled pathway that achieved a 120-fold increase in pathway productivity in a heterologous streptomycete host. Additionally, an unexpected biosynthetic bottleneck resulted in the production of a suite of new bottromycin-related metabolites.
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Affiliation(s)
- Tom H. Eyles
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, U.K
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, U.K
| | - Andrew W. Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, U.K
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Zeng F, Zang J, Zhang S, Hao Z, Dong J, Lin Y. AFEAP cloning: a precise and efficient method for large DNA sequence assembly. BMC Biotechnol 2017; 17:81. [PMID: 29137618 PMCID: PMC5686892 DOI: 10.1186/s12896-017-0394-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/30/2017] [Indexed: 11/12/2022] Open
Abstract
Background Recent development of DNA assembly technologies has spurred myriad advances in synthetic biology, but new tools are always required for complicated scenarios. Here, we have developed an alternative DNA assembly method named AFEAP cloning (Assembly of Fragment Ends After PCR), which allows scarless, modular, and reliable construction of biological pathways and circuits from basic genetic parts. Methods The AFEAP method requires two-round of PCRs followed by ligation of the sticky ends of DNA fragments. The first PCR yields linear DNA fragments and is followed by a second asymmetric (one primer) PCR and subsequent annealing that inserts overlapping overhangs at both sides of each DNA fragment. The overlapping overhangs of the neighboring DNA fragments annealed and the nick was sealed by T4 DNA ligase, followed by bacterial transformation to yield the desired plasmids. Results We characterized the capability and limitations of new developed AFEAP cloning and demonstrated its application to assemble DNA with varying scenarios. Under the optimized conditions, AFEAP cloning allows assembly of an 8 kb plasmid from 1-13 fragments with high accuracy (between 80 and 100%), and 8.0, 11.6, 19.6, 28, and 35.6 kb plasmids from five fragments at 91.67, 91.67, 88.33, 86.33, and 81.67% fidelity, respectively. AFEAP cloning also is capable to construct bacterial artificial chromosome (BAC, 200 kb) with a fidelity of 46.7%. Conclusions AFEAP cloning provides a powerful, efficient, seamless, and sequence-independent DNA assembly tool for multiple fragments up to 13 and large DNA up to 200 kb that expands synthetic biologist’s toolbox. Electronic supplementary material The online version of this article (doi: 10.1186/s12896-017-0394-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fanli Zeng
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, People's Republic of China
| | - Jinping Zang
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, People's Republic of China
| | - Suhua Zhang
- Institute of Biophysics, Hebei University of Technology, Tianjin, 300401, People's Republic of China
| | - Zhimin Hao
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, People's Republic of China
| | - Jingao Dong
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, People's Republic of China.
| | - Yibin Lin
- McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, 77030, USA.
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Decoene T, De Paepe B, Maertens J, Coussement P, Peters G, De Maeseneire SL, De Mey M. Standardization in synthetic biology: an engineering discipline coming of age. Crit Rev Biotechnol 2017; 38:647-656. [PMID: 28954542 DOI: 10.1080/07388551.2017.1380600] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Leaping DNA read-and-write technologies, and extensive automation and miniaturization are radically transforming the field of biological experimentation by providing the tools that enable the cost-effective high-throughput required to address the enormous complexity of biological systems. However, standardization of the synthetic biology workflow has not kept abreast with dwindling technical and resource constraints, leading, for example, to the collection of multi-level and multi-omics large data sets that end up disconnected or remain under- or even unexploited. PURPOSE In this contribution, we critically evaluate the various efforts, and the (limited) success thereof, in order to introduce standards for defining, designing, assembling, characterizing, and sharing synthetic biology parts. The causes for this success or the lack thereof, as well as possible solutions to overcome these, are discussed. CONCLUSION Akin to other engineering disciplines, extensive standardization will undoubtedly speed-up and reduce the cost of bioprocess development. In this respect, further implementation of synthetic biology standards will be crucial for the field in order to redeem its promise, i.e. to enable predictable forward engineering.
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Affiliation(s)
- Thomas Decoene
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
| | - Brecht De Paepe
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
| | - Jo Maertens
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
| | | | - Gert Peters
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
| | - Sofie L De Maeseneire
- b InBio.be, Centre for Industrial Biotechnology and Biocatalysis, Ghent University , Ghent , Belgium
| | - Marjan De Mey
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
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