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Anhel AM, Alejaldre L, Goñi-Moreno Á. The Laboratory Automation Protocol (LAP) Format and Repository: A Platform for Enhancing Workflow Efficiency in Synthetic Biology. ACS Synth Biol 2023; 12:3514-3520. [PMID: 37982688 PMCID: PMC7615385 DOI: 10.1021/acssynbio.3c00397] [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] [Indexed: 11/21/2023]
Abstract
Laboratory automation deals with eliminating manual tasks in high-throughput protocols. It therefore plays a crucial role in allowing fast and reliable synthetic biology. However, implementing open-source automation solutions often demands experimental scientists to possess scripting skills, and even when they do, there is no standardized toolkit available for their use. To address this, we present the Laboratory Automation Protocol (LAP) Format and Repository. LAPs adhere to a standardized script-based format, enhancing end-user implementation and simplifying further development. With a modular design, LAPs can be seamlessly combined to create customized, target-specific workflows. Furthermore, all LAPs undergo experimental validation, ensuring their reliability. Detailed information is provided within each repository entry, allowing users to validate the LAPs in their own laboratory settings. We advocate for the adoption of the LAP Format and Repository as a community resource, which will continue to expand, improving the reliability and reproducibility of the automation processes.
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Affiliation(s)
- Ana-Mariya Anhel
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), 28223, Madrid, Spain
| | - Lorea Alejaldre
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), 28223, Madrid, Spain
| | - Ángel Goñi-Moreno
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), 28223, Madrid, Spain
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2
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Script-based automation of analytical instrument software tasks. SLAS Technol 2022; 27:209-213. [DOI: 10.1016/j.slast.2021.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Luo Y, James JS, Jones S, Martella A, Cai Y. EMMA-CAD: Design Automation for Synthetic Mammalian Constructs. ACS Synth Biol 2022; 11:579-586. [PMID: 35050610 DOI: 10.1021/acssynbio.1c00433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Computational design tools are the cornerstone of synthetic biology and have underpinned its rapid development over the past two decades. As the field has matured, the scale of biological investigation has expanded dramatically, and researchers often must rely on computational tools to operate in the high-throughput investigational space. This is especially apparent in the modular design of DNA expression circuits, where complexity is accumulated rapidly. Alongside our automated pipeline for the high-throughput construction of Extensible Modular Mammalian Assembly (EMMA) expression vectors, we recognized the need for an integrated software solution for EMMA vector design. Here we present EMMA-CAD (https://emma.cailab.org), a powerful web-based computer-aided design tool for the rapid design of bespoke mammalian expression vectors. EMMA-CAD features a variety of functionalities, including a user-friendly design interface, automated connector selection underpinned by rigorous computer optimization algorithms, customization of part libraries, and personalized design spaces. Capable of translating vector assembly designs into human- and machine-readable protocols for vector construction, EMMA-CAD integrates seamlessly into our automated EMMA pipeline, hence completing an end-to-end design to production workflow.
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Affiliation(s)
- Yisha Luo
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Joshua S. James
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Sally Jones
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, U.K
| | - Andrea Martella
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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4
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James JS, Jones S, Martella A, Luo Y, Fisher DI, Cai Y. Automation and Expansion of EMMA Assembly for Fast-Tracking Mammalian System Engineering. ACS Synth Biol 2022; 11:587-595. [PMID: 35061373 DOI: 10.1021/acssynbio.1c00330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With applications from functional genomics to the production of therapeutic biologics, libraries of mammalian expression vectors have become a cornerstone of modern biological investigation and engineering. Multiple modular vector platforms facilitate the rapid design and assembly of vectors. However, such systems approach a technical bottleneck when a library of bespoke vectors is required. Utilizing the flexibility and robustness of the Extensible Mammalian Modular Assembly (EMMA) toolkit, we present an automated workflow for the library-scale design, assembly, and verification of mammalian expression vectors. Vector design is simplified using our EMMA computer-aided design tool (EMMA-CAD), while the precision and speed of acoustic droplet ejection technology are applied in vector assembly. Our pipeline facilitates significant reductions in both reagent usage and researcher hands-on time compared with manual assembly, as shown by system Q-metrics. To demonstrate automated EMMA performance, we compiled a library of 48 distinct plasmid vectors encoding either CRISPR interference or activation modalities. Characterization of the workflow parameters shows that high assembly efficiency is maintained across vectors of various sizes and design complexities. Our system also performs strongly compared with manual assembly efficiency benchmarks. Alongside our automated pipeline, we present a straightforward strategy for integrating gRNA and Cas modules into the EMMA platform, enabling the design and manufacture of valuable genome editing resources.
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Affiliation(s)
- Joshua S James
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Sally Jones
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, U.K
| | - Andrea Martella
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Yisha Luo
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - David I Fisher
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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5
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Raj K, Venayak N, Diep P, Golla SA, Yakunin AF, Mahadevan R. Automation assisted anaerobic phenotyping for metabolic engineering. Microb Cell Fact 2021; 20:184. [PMID: 34556155 PMCID: PMC8461876 DOI: 10.1186/s12934-021-01675-3] [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: 05/17/2021] [Accepted: 09/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microorganisms can be metabolically engineered to produce a wide range of commercially important chemicals. Advancements in computational strategies for strain design and synthetic biological techniques to construct the designed strains have facilitated the generation of large libraries of potential candidates for chemical production. Consequently, there is a need for high-throughput laboratory scale techniques to characterize and screen these candidates to select strains for further investigation in large scale fermentation processes. Several small-scale fermentation techniques, in conjunction with laboratory automation have enhanced the throughput of enzyme and strain phenotyping experiments. However, such high throughput experimentation typically entails large operational costs and generate massive amounts of laboratory plastic waste. RESULTS In this work, we develop an eco-friendly automation workflow that effectively calibrates and decontaminates fixed-tip liquid handling systems to reduce tip waste. We also investigate inexpensive methods to establish anaerobic conditions in microplates for high-throughput anaerobic phenotyping. To validate our phenotyping platform, we perform two case studies-an anaerobic enzyme screen, and a microbial phenotypic screen. We used our automation platform to investigate conditions under which several strains of E. coli exhibit the same phenotypes in 0.5 L bioreactors and in our scaled-down fermentation platform. We also propose the use of dimensionality reduction through t-distributed stochastic neighbours embedding (t-SNE) in conjunction with our phenotyping platform to effectively cluster similarly performing strains at the bioreactor scale. CONCLUSIONS Fixed-tip liquid handling systems can significantly reduce the amount of plastic waste generated in biological laboratories and our decontamination and calibration protocols could facilitate the widespread adoption of such systems. Further, the use of t-SNE in conjunction with our automation platform could serve as an effective scale-down model for bioreactor fermentations. Finally, by integrating an in-house data-analysis pipeline, we were able to accelerate the 'test' phase of the design-build-test-learn cycle of metabolic engineering.
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Affiliation(s)
- Kaushik Raj
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Sai Akhil Golla
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
- School of Natural Sciences, Bangor University, Bangor, LL57 2DG UK
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, M5S 3G9 Canada
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6
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Wang J, Sui X, Ding Y, Fu Y, Feng X, Liu M, Zhang Y, Xian M, Zhao G. A fast and robust iterative genome-editing method based on a Rock-Paper-Scissors strategy. Nucleic Acids Res 2021; 49:e12. [PMID: 33270888 PMCID: PMC7826264 DOI: 10.1093/nar/gkaa1141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/28/2020] [Accepted: 11/07/2020] [Indexed: 01/22/2023] Open
Abstract
The production of optimized strains of a specific phenotype requires the construction and testing of a large number of genome modifications and combinations thereof. Most bacterial iterative genome-editing methods include essential steps to eliminate selection markers, or to cure plasmids. Additionally, the presence of escapers leads to time-consuming separate single clone picking and subsequent cultivation steps. Herein, we report a genome-editing method based on a Rock-Paper-Scissors (RPS) strategy. Each of three constructed sgRNA plasmids can cure, or be cured by, the other two plasmids in the system; plasmids from a previous round of editing can be cured while the current round of editing takes place. Due to the enhanced curing efficiency and embedded double check mechanism, separate steps for plasmid curing or confirmation are not necessary, and only two times of cultivation are needed per genome-editing round. This method was successfully demonstrated in Escherichia coli and Klebsiella pneumoniae with both gene deletions and replacements. To the best of our knowledge, this is the fastest and most robust iterative genome-editing method, with the least times of cultivation decreasing the possibilities of spontaneous genome mutations.
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Affiliation(s)
- Jichao Wang
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Xinyue Sui
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yamei Ding
- Institute of Oceanology, Chinese Academy of Sciences, 266071 Qingdao, China
| | - Yingxin Fu
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Xinjun Feng
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Min Liu
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Guang Zhao
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
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7
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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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8
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Goyal G, Elsbree N, Fero M, Hillson NJ, Linshiz G. Repurposing a microfluidic formulation device for automated DNA construction. PLoS One 2020; 15:e0242157. [PMID: 33175889 PMCID: PMC7657503 DOI: 10.1371/journal.pone.0242157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/27/2020] [Indexed: 11/19/2022] Open
Abstract
Microfluidic applications have expanded greatly over the past decade. For the most part, however, each microfluidics platform is developed with a specific task in mind, rather than as a general-purpose device with a wide-range of functionality. Here, we show how a microfluidic system, originally developed to investigate protein phase behavior, can be modified and repurposed for another application, namely DNA construction. We added new programable controllers to direct the flow of reagents across the chip. We designed the assembly of a combinatorial Golden Gate DNA library using TeselaGen DESIGN software and used the repurposed microfluidics platform to assemble the designed library from off-chip prepared DNA assembly pieces. Further experiments verified the sequences and function of the on-chip assembled DNA constructs.
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Affiliation(s)
- Garima Goyal
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Nick Elsbree
- TeselaGen Biotechnology, San Francisco, California, United States of America
| | - Michael Fero
- TeselaGen Biotechnology, San Francisco, California, United States of America
| | - Nathan J. Hillson
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Gregory Linshiz
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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9
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Rajakumar PD, Gowers GOF, Suckling L, Foster A, Ellis T, Kitney RI, McClymont DW, Freemont PS. Rapid Prototyping Platform for Saccharomyces cerevisiae Using Computer-Aided Genetic Design Enabled by Parallel Software and Workcell Platform Development. SLAS Technol 2018; 24:291-297. [DOI: 10.1177/2472630318798304] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Biofoundries have enabled the ability to automate the construction of genetic constructs using computer-aided design. In this study, we have developed the methodology required to abstract and automate the construction of yeast-compatible designs. We demonstrate the use of our in-house software tool, AMOS, to coordinate with design software, JMP, and robotic liquid handling platforms to successfully manage the construction of a library of 88 yeast expression plasmids. In this proof-of-principle study, we used three fluorescent genes as proxy for three enzyme coding sequences. Our platform has been designed to quickly iterate around a design cycle of four protein coding sequences per plasmid, with larger numbers possible with multiplexed genome integrations in Saccharomyces cerevisiae. This work highlights how developing scalable new biotechnology applications requires a close integration between software development, liquid handling robotics, and protocol development.
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Affiliation(s)
| | - G-O. F. Gowers
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - L. Suckling
- The London DNA Foundry, Imperial College London, London, UK
| | - A. Foster
- The London DNA Foundry, Imperial College London, London, UK
| | - T. Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - R. I. Kitney
- The London DNA Foundry, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | | | - P. S. Freemont
- The London DNA Foundry, Imperial College London, London, UK
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
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10
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Vazquez-Vilar M, Orzaez D, Patron N. DNA assembly standards: Setting the low-level programming code for plant biotechnology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:33-41. [PMID: 29907307 DOI: 10.1016/j.plantsci.2018.02.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 05/28/2023]
Abstract
Synthetic Biology is defined as the application of engineering principles to biology. It aims to increase the speed, ease and predictability with which desirable changes and novel traits can be conferred to living cells. The initial steps in this process aim to simplify the encoding of new instructions in DNA by establishing low-level programming languages for biology. Together with advances in the laboratory that allow multiple DNA molecules to be efficiently assembled together into a desired order in a single step, this approach has simplified the design and assembly of multigene constructs and has even facilitated the automated construction of synthetic chromosomes. These advances and technologies are now being applied to plants, for which there are a growing number of software and wetware tools for the design, construction and delivery of DNA molecules and for the engineering of endogenous genes. Here we review the efforts of the past decade that have established synthetic biology workflows and tools for plants and discuss the constraints and bottlenecks of this emerging field.
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Affiliation(s)
- Marta Vazquez-Vilar
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Spain.
| | - Nicola Patron
- Department of Engineering Biology, The Earlham Institute, Norwich Research Park, Norfolk, NR1 7UZ, UK.
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11
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Eriksen DT, Chao R, Zhao H. Applying Advanced DNA Assembly Methods to Generate Pathway Libraries. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Dawn T. Eriksen
- University of Illinois at Urbana-Champaign; Department of Chemical and Biomolecular Engineering; 600 South Mathews Avenue, Urbana IL 61801 USA
| | - Ran Chao
- University of Illinois at Urbana-Champaign; Department of Chemical and Biomolecular Engineering; 600 South Mathews Avenue, Urbana IL 61801 USA
| | - Huimin Zhao
- University of Illinois at Urbana-Champaign; Department of Chemical and Biomolecular Engineering; 600 South Mathews Avenue, Urbana IL 61801 USA
- University of Illinois at Urbana-Champaign; Departments of Chemistry, Biochemistry, and Bioengineering, 600 South Mathews Avenue; Urbana IL 61801 USA
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12
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Whitehead E, Rudolf F, Kaltenbach HM, Stelling J. Automated Planning Enables Complex Protocols on Liquid-Handling Robots. ACS Synth Biol 2018; 7:922-932. [PMID: 29486123 DOI: 10.1021/acssynbio.8b00021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Robotic automation in synthetic biology is especially relevant for liquid handling to facilitate complex experiments. However, research tasks that are not highly standardized are still rarely automated in practice. Two main reasons for this are the substantial investments required to translate molecular biological protocols into robot programs, and the fact that the resulting programs are often too specific to be easily reused and shared. Recent developments of standardized protocols and dedicated programming languages for liquid-handling operations addressed some aspects of ease-of-use and portability of protocols. However, either they focus on simplicity, at the expense of enabling complex protocols, or they entail detailed programming, with corresponding skills and efforts required from the users. To reconcile these trade-offs, we developed Roboliq, a software system that uses artificial intelligence (AI) methods to integrate (i) generic formal, yet intuitive, protocol descriptions, (ii) complete, but usually hidden, programming capabilities, and (iii) user-system interactions to automatically generate executable, optimized robot programs. Roboliq also enables high-level specifications of complex tasks with conditional execution. To demonstrate the system's benefits for experiments that are difficult to perform manually because of their complexity, duration, or time-critical nature, we present three proof-of-principle applications for the reproducible, quantitative characterization of GFP variants.
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Affiliation(s)
- Ellis Whitehead
- Department of Biosystems Science and Engineering, ETH Zurich and SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering, ETH Zurich and SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Hans-Michael Kaltenbach
- Department of Biosystems Science and Engineering, ETH Zurich and SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering, ETH Zurich and SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
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13
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Dossani ZY, Reider Apel A, Szmidt-Middleton H, Hillson NJ, Deutsch S, Keasling JD, Mukhopadhyay A. A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering. Yeast 2017; 35:273-280. [PMID: 29084380 PMCID: PMC5873372 DOI: 10.1002/yea.3292] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/08/2017] [Accepted: 10/19/2017] [Indexed: 12/28/2022] Open
Abstract
Despite the need for inducible promoters in strain development efforts, the majority of engineering in Saccharomyces cerevisiae continues to rely on a few constitutively active or inducible promoters. Building on advances that use the modular nature of both transcription factors and promoter regions, we have built a library of hybrid promoters that are regulated by a synthetic transcription factor. The hybrid promoters consist of native S. cerevisiae promoters, in which the operator regions have been replaced with sequences that are recognized by the bacterial LexA DNA binding protein. Correspondingly, the synthetic transcription factor (TF) consists of the DNA binding domain of the LexA protein, fused with the human estrogen binding domain and the viral activator domain, VP16. The resulting system with a bacterial DNA binding domain avoids the transcription of native S. cerevisiae genes, and the hybrid promoters can be induced using estradiol, a compound with no detectable impact on S. cerevisiae physiology. Using combinations of one, two or three operator sequence repeats and a set of native S. cerevisiae promoters, we obtained a series of hybrid promoters that can be induced to different levels, using the same synthetic TF and a given estradiol. This set of promoters, in combination with our synthetic TF, has the potential to regulate numerous genes or pathways simultaneously, to multiple desired levels, in a single strain.
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Affiliation(s)
- Zain Y Dossani
- DOE Joint Bioenergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amanda Reider Apel
- DOE Joint Bioenergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Heather Szmidt-Middleton
- DOE Joint Bioenergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nathan J Hillson
- DOE Joint Bioenergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,DOE Joint Genome Institute, Walnut Creek, California, USA.,DOE Agile BioFoundry, Emeryville, California, USA
| | - Samuel Deutsch
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,DOE Joint Genome Institute, Walnut Creek, California, USA.,DOE Agile BioFoundry, Emeryville, California, USA
| | - Jay D Keasling
- DOE Joint Bioenergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220 Kemitorvet, 2800Kgs, Lyngby, Denmark
| | - Aindrila Mukhopadhyay
- DOE Joint Bioenergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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14
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Bhatia SP, Smanski MJ, Voigt CA, Densmore DM. Genetic Design via Combinatorial Constraint Specification. ACS Synth Biol 2017; 6:2130-2135. [PMID: 28874044 DOI: 10.1021/acssynbio.7b00154] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We present a formal language for specifying via constraints a "design space" of DNA constructs composed of genetic parts, and an algorithm for automatically and correctly creating a novel representation of the space of satisfying designs. The language is simple, captures a large class of design spaces, and possesses algorithms for common operations on design spaces. The flexibility of this approach is demonstrated using a 16-gene nitrogen fixation pathway and genetic logic circuits.
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Affiliation(s)
- Swapnil P. Bhatia
- Biological
Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Michael J. Smanski
- Department
of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St Paul, Minnesota 55108, United States
| | - Christopher A. Voigt
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Douglas M. Densmore
- Biological
Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
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15
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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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16
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Needs and opportunities in bio-design automation: four areas for focus. Curr Opin Chem Biol 2017; 40:111-118. [PMID: 28923279 DOI: 10.1016/j.cbpa.2017.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/19/2017] [Accepted: 08/22/2017] [Indexed: 11/21/2022]
Abstract
Bio-design automation (BDA) is an emerging field focused on computer-aided design, engineering principles, and automated manufacturing of biological systems. Here we discuss some outstanding challenges for bio-design that can be addressed by developing new tools for combinatorial engineering, equipment interfacing, next-generation sequencing, and workflow integration. These four areas, while not an exhaustive list of those that need to be addressed, could yield advances in bio-design, laboratory automation, and biometrology.
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17
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Gupta V, Irimia J, Pau I, Rodríguez-Patón A. BioBlocks: Programming Protocols in Biology Made Easier. ACS Synth Biol 2017; 6:1230-1232. [PMID: 28051850 DOI: 10.1021/acssynbio.6b00304] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The methods to execute biological experiments are evolving. Affordable fluid handling robots and on-demand biology enterprises are making automating entire experiments a reality. Automation offers the benefit of high-throughput experimentation, rapid prototyping, and improved reproducibility of results. However, learning to automate and codify experiments is a difficult task as it requires programming expertise. Here, we present a web-based visual development environment called BioBlocks for describing experimental protocols in biology. It is based on Google's Blockly and Scratch, and requires little or no experience in computer programming to automate the execution of experiments. The experiments can be specified, saved, modified, and shared between multiple users in an easy manner. BioBlocks is open-source and can be customized to execute protocols on local robotic platforms or remotely, that is, in the cloud. It aims to serve as a de facto open standard for programming protocols in Biology.
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Affiliation(s)
- Vishal Gupta
- Departamento de Inteligencia
Artificial, Universidad Politécnica de Madrid. Campus de Montegancedo, Boadilla del Monte
(Madrid), 28660, Spain
| | - Jesús Irimia
- Departamento de Inteligencia
Artificial, Universidad Politécnica de Madrid. Campus de Montegancedo, Boadilla del Monte
(Madrid), 28660, Spain
| | - Iván Pau
- Departamento de Inteligencia
Artificial, Universidad Politécnica de Madrid. Campus de Montegancedo, Boadilla del Monte
(Madrid), 28660, Spain
| | - Alfonso Rodríguez-Patón
- Departamento de Inteligencia
Artificial, Universidad Politécnica de Madrid. Campus de Montegancedo, Boadilla del Monte
(Madrid), 28660, Spain
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18
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19
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Zhao D, Yuan S, Xiong B, Sun H, Ye L, Li J, Zhang X, Bi C. Development of a fast and easy method for Escherichia coli genome editing with CRISPR/Cas9. Microb Cell Fact 2016; 15:205. [PMID: 27908280 PMCID: PMC5134288 DOI: 10.1186/s12934-016-0605-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 11/25/2016] [Indexed: 11/24/2022] Open
Abstract
Background Microbial genome editing is a powerful tool to modify chromosome in way of deletion, insertion or replacement, which is one of the most important techniques in metabolic engineering research. The emergence of CRISPR/Cas9 technique inspires various genomic editing methods. Results In this research, the goal of development of a fast and easy method for Escherichia coli genome editing with high efficiency is pursued. For this purpose, we designed modular plasmid assembly strategy, compared effects of different length of homologous arms for recombination, and tested different sets of recombinases. The final technique we developed only requires one plasmid construction and one transformation of practice to edit a genomic locus with 3 days and minimal lab work. In addition, the single temperature sensitive plasmid is easy to eliminate for another round of editing. Especially, process of the modularized editing plasmid construction only takes 4 h. Conclusion In this study, we developed a fast and easy genome editing procedure based on CRISPR/Cas9 system that only required the work of one plasmid construction and one transformation, which allowed modification of a chromosome locus within 3 days and could be performed continuously for multiple loci. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0605-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Shenli Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Bin Xiong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Hongnian Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Lijun Ye
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Jing Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China.
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20
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Managing bioengineering complexity with AI techniques. Biosystems 2016; 148:40-46. [DOI: 10.1016/j.biosystems.2015.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 08/03/2015] [Accepted: 08/14/2015] [Indexed: 11/22/2022]
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21
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Beal J, Haddock-Angelli T, Gershater M, de Mora K, Lizarazo M, Hollenhorst J, Rettberg R. Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli. PLoS One 2016; 11:e0150182. [PMID: 26937966 PMCID: PMC4777433 DOI: 10.1371/journal.pone.0150182] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/10/2016] [Indexed: 11/18/2022] Open
Abstract
We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1.54-fold standard deviation for the ratio between strong promoters to 5.75-fold for the ratio between the strongest and weakest promoter, and while host strain did not affect expression ratios, choice of instrument did. This result shows that high quantitative precision and reproducibility of results is possible, while at the same time indicating areas needing improved laboratory practices.
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Affiliation(s)
- Jacob Beal
- Raytheon BBN Technologies, Cambridge, MA, United States of America
- * E-mail:
| | | | | | - Kim de Mora
- iGEM Foundation, Cambridge, MA, United States of America
| | | | | | - Randy Rettberg
- iGEM Foundation, Cambridge, MA, United States of America
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22
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Forry SP, Madonna MC, López-Pérez D, Lin NJ, Pasco MD. Automation of antimicrobial activity screening. AMB Express 2016; 6:20. [PMID: 26970766 PMCID: PMC4788993 DOI: 10.1186/s13568-016-0191-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 02/23/2016] [Indexed: 11/10/2022] Open
Abstract
Manual and automated methods were compared for routine screening of compounds for antimicrobial activity. Automation generally accelerated assays and required less user intervention while producing comparable results. Automated protocols were validated for planktonic, biofilm, and agar cultures of the oral microbe Streptococcus mutans that is commonly associated with tooth decay. Toxicity assays for the known antimicrobial compound cetylpyridinium chloride (CPC) were validated against planktonic, biofilm forming, and 24 h biofilm culture conditions, and several commonly reported toxicity/antimicrobial activity measures were evaluated: the 50 % inhibitory concentration (IC50), the minimum inhibitory concentration (MIC), and the minimum bactericidal concentration (MBC). Using automated methods, three halide salts of cetylpyridinium (CPC, CPB, CPI) were rapidly screened with no detectable effect of the counter ion on antimicrobial activity.
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Affiliation(s)
- Samuel P. Forry
- />Biosystems and Biomaterials Division, National Institutes of Standard and Technology, Gaithersburg, MD 20899 USA
| | - Megan C. Madonna
- />Biosystems and Biomaterials Division, National Institutes of Standard and Technology, Gaithersburg, MD 20899 USA
| | - Daneli López-Pérez
- />Biosystems and Biomaterials Division, National Institutes of Standard and Technology, Gaithersburg, MD 20899 USA
- />Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993 USA
| | - Nancy J. Lin
- />Biosystems and Biomaterials Division, National Institutes of Standard and Technology, Gaithersburg, MD 20899 USA
| | - Madeleine D. Pasco
- />Biosystems and Biomaterials Division, National Institutes of Standard and Technology, Gaithersburg, MD 20899 USA
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23
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Linshiz G, Jensen E, Stawski N, Bi C, Elsbree N, Jiao H, Kim J, Mathies R, Keasling JD, Hillson NJ. End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis. J Biol Eng 2016; 10:3. [PMID: 26839585 PMCID: PMC4736182 DOI: 10.1186/s13036-016-0024-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/04/2016] [Indexed: 01/06/2023] Open
Abstract
Background Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. Results Herein, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, and proteogenic and metabolic output analysis. Conclusions Taken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis. Electronic supplementary material The online version of this article (doi:10.1186/s13036-016-0024-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregory Linshiz
- Fuels Synthesis and Technologies Divisions, Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, CA 94720 USA ; DNA Synthesis Science Program, DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Erik Jensen
- Chemistry Department, University of California, Berkeley, CA 94720 USA ; HJ Science & Technology Inc., Berkeley, CA 94710 USA
| | - Nina Stawski
- Fuels Synthesis and Technologies Divisions, Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, CA 94720 USA
| | - Changhao Bi
- Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, CA 94720 USA ; Present address: Tianjin Institute of Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Nick Elsbree
- Fuels Synthesis and Technologies Divisions, Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, CA 94720 USA
| | - Hong Jiao
- HJ Science & Technology Inc., Berkeley, CA 94710 USA
| | - Jungkyu Kim
- Chemistry Department, University of California, Berkeley, CA 94720 USA ; Present address: Department of Mechanical Engineering, Texas Tech University, Lubbock, TX 79409 USA
| | - Richard Mathies
- Chemistry Department, University of California, Berkeley, CA 94720 USA
| | - Jay D Keasling
- Fuels Synthesis and Technologies Divisions, Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, CA 94720 USA ; Department of Chemical & Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Nathan J Hillson
- Fuels Synthesis and Technologies Divisions, Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, CA 94720 USA ; DNA Synthesis Science Program, DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
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24
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Li S, Si T, Wang M, Zhao H. Development of a Synthetic Malonyl-CoA Sensor in Saccharomyces cerevisiae for Intracellular Metabolite Monitoring and Genetic Screening. ACS Synth Biol 2015; 4:1308-15. [PMID: 26149896 DOI: 10.1021/acssynbio.5b00069] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Genetic sensors capable of converting key metabolite levels to fluorescence signals enable the monitoring of intracellular compound concentrations in living cells, and emerge as an efficient tool in high-throughput genetic screening. However, the development of genetic sensors in yeasts lags far behind their development in bacteria. Here we report the design of a malonyl-CoA sensor in Saccharomyces cerevisiae using an adapted bacterial transcription factor FapR and its corresponding operator fapO to gauge intracellular malonyl-CoA levels. By combining this sensor with a genome-wide overexpression library, we identified two novel gene targets that improved intracellular malonyl-CoA concentration. We further utilized the resulting recombinant yeast strain to produce a valuable compound, 3-hydroxypropionic acid, from malonyl-CoA and enhanced its titer by 120%. Such a genetic sensor provides a powerful approach for genome-wide screening and could further improve the synthesis of a large range of chemicals derived from malonyl-CoA in yeast.
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Affiliation(s)
- Sijin Li
- Energy Biosciences Institute, ‡Institute for Genomic Biology, §Department of Chemical
and Biomolecular Engineering, and ∥Departments of Chemistry, Biochemistry, and
Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Tong Si
- Energy Biosciences Institute, ‡Institute for Genomic Biology, §Department of Chemical
and Biomolecular Engineering, and ∥Departments of Chemistry, Biochemistry, and
Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Meng Wang
- Energy Biosciences Institute, ‡Institute for Genomic Biology, §Department of Chemical
and Biomolecular Engineering, and ∥Departments of Chemistry, Biochemistry, and
Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Energy Biosciences Institute, ‡Institute for Genomic Biology, §Department of Chemical
and Biomolecular Engineering, and ∥Departments of Chemistry, Biochemistry, and
Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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25
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Sadowski MI, Grant C, Fell TS. Harnessing QbD, Programming Languages, and Automation for Reproducible Biology. Trends Biotechnol 2015; 34:214-227. [PMID: 26708960 DOI: 10.1016/j.tibtech.2015.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/16/2015] [Accepted: 11/19/2015] [Indexed: 12/18/2022]
Abstract
Building robust manufacturing processes from biological components is a task that is highly complex and requires sophisticated tools to describe processes, inputs, and measurements and administrate management of knowledge, data, and materials. We argue that for bioengineering to fully access biological potential, it will require application of statistically designed experiments to derive detailed empirical models of underlying systems. This requires execution of large-scale structured experimentation for which laboratory automation is necessary. This requires development of expressive, high-level languages that allow reusability of protocols, characterization of their reliability, and a change in focus from implementation details to functional properties. We review recent developments in these areas and identify what we believe is an exciting trend that promises to revolutionize biotechnology.
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Affiliation(s)
- Michael I Sadowski
- Synthace Limited, London Bioscience Innovation Centre, 2 Royal College St, London NW1 0NH, UK
| | - Chris Grant
- Synthace Limited, London Bioscience Innovation Centre, 2 Royal College St, London NW1 0NH, UK
| | - Tim S Fell
- Synthace Limited, London Bioscience Innovation Centre, 2 Royal College St, London NW1 0NH, UK.
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26
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Shih SCC, Goyal G, Kim PW, Koutsoubelis N, Keasling JD, Adams PD, Hillson NJ, Singh AK. A Versatile Microfluidic Device for Automating Synthetic Biology. ACS Synth Biol 2015; 4:1151-64. [PMID: 26075958 DOI: 10.1021/acssynbio.5b00062] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New microbes are being engineered that contain the genetic circuitry, metabolic pathways, and other cellular functions required for a wide range of applications such as producing biofuels, biobased chemicals, and pharmaceuticals. Although currently available tools are useful in improving the synthetic biology process, further improvements in physical automation would help to lower the barrier of entry into this field. We present an innovative microfluidic platform for assembling DNA fragments with 10× lower volumes (compared to that of current microfluidic platforms) and with integrated region-specific temperature control and on-chip transformation. Integration of these steps minimizes the loss of reagents and products compared to that with conventional methods, which require multiple pipetting steps. For assembling DNA fragments, we implemented three commonly used DNA assembly protocols on our microfluidic device: Golden Gate assembly, Gibson assembly, and yeast assembly (i.e., TAR cloning, DNA Assembler). We demonstrate the utility of these methods by assembling two combinatorial libraries of 16 plasmids each. Each DNA plasmid is transformed into Escherichia coli or Saccharomyces cerevisiae using on-chip electroporation and further sequenced to verify the assembly. We anticipate that this platform will enable new research that can integrate this automated microfluidic platform to generate large combinatorial libraries of plasmids and will help to expedite the overall synthetic biology process.
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Affiliation(s)
- Steve C. C. Shih
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Garima Goyal
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Peter W. Kim
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Nicolas Koutsoubelis
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Paul D. Adams
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Nathan J. Hillson
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Anup K. Singh
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
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27
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Beal J. Signal-to-Noise Ratio Measures Efficacy of Biological Computing Devices and Circuits. Front Bioeng Biotechnol 2015; 3:93. [PMID: 26177070 PMCID: PMC4485182 DOI: 10.3389/fbioe.2015.00093] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/15/2015] [Indexed: 11/13/2022] Open
Abstract
Engineering biological cells to perform computations has a broad range of important potential applications, including precision medical therapies, biosynthesis process control, and environmental sensing. Implementing predictable and effective computation, however, has been extremely difficult to date, due to a combination of poor composability of available parts and of insufficient characterization of parts and their interactions with the complex environment in which they operate. In this paper, the author argues that this situation can be improved by quantitative signal-to-noise analysis of the relationship between computational abstractions and the variation and uncertainty endemic in biological organisms. This analysis takes the form of a ΔSNRdB function for each computational device, which can be computed from measurements of a device's input/output curve and expression noise. These functions can then be combined to predict how well a circuit will implement an intended computation, as well as evaluating the general suitability of biological devices for engineering computational circuits. Applying signal-to-noise analysis to current repressor libraries shows that no library is currently sufficient for general circuit engineering, but also indicates key targets to remedy this situation and vastly improve the range of computations that can be used effectively in the implementation of biological applications.
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Affiliation(s)
- Jacob Beal
- Raytheon BBN Technologies, Cambridge, MA, USA
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28
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Beal J. Bridging the gap: a roadmap to breaking the biological design barrier. Front Bioeng Biotechnol 2015; 2:87. [PMID: 25654077 PMCID: PMC4299508 DOI: 10.3389/fbioe.2014.00087] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/21/2014] [Indexed: 12/11/2022] Open
Abstract
This paper presents an analysis of an emerging bottleneck in organism engineering, and paths by which it may be overcome. Recent years have seen the development of a profusion of synthetic biology tools, largely falling into two categories: high-level “design” tools aimed at mapping from organism specifications to nucleic acid sequences implementing those specifications, and low-level “build and test” tools aimed at faster, cheaper, and more reliable fabrication of those sequences and assays of their behavior in engineered biological organisms. Between the two families, however, there is a major gap: we still largely lack the predictive models and component characterization data required to effectively determine which of the many possible candidate sequences considered in the design phase are the most likely to produce useful results when built and tested. As low-level tools continue to mature, the bottleneck in biological systems engineering is shifting to be dominated by design, making this gap a critical barrier to progress. Considering how to address this gap, we find that widespread adoption of readily available analytic and assay methods is likely to lead to rapid improvement in available predictive models and component characterization models, as evidenced by a number of recent results. Such an enabling development is, in turn, likely to allow high-level tools to break the design barrier and support rapid development of transformative biological applications.
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Affiliation(s)
- Jacob Beal
- Raytheon BBN Technologies , Cambridge, MA , USA
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29
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Chao R, Yuan Y, Zhao H. Recent advances in DNA assembly technologies. FEMS Yeast Res 2015; 15:1-9. [PMID: 24903193 DOI: 10.1111/1567-1364.12171] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/02/2014] [Accepted: 05/27/2014] [Indexed: 11/28/2022] Open
Abstract
DNA assembly is one of the most important foundational technologies for synthetic biology and metabolic engineering. Since the development of the restriction digestion and ligation method in the early 1970s, a significant amount of effort has been devoted to developing better DNA assembly methods with higher efficiency, fidelity, and modularity, as well as simpler and faster protocols. This review will not only summarize the key DNA assembly methods and their recent applications, but also highlight the innovations in assembly schemes and the challenges in automating the DNA assembly methods.
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Affiliation(s)
- Ran Chao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaig, Urbana, IL, USA
| | - Yongbo Yuan
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaig, Urbana, IL, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaig, Urbana, IL, USA .,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Poust S, Hagen A, Katz L, Keasling JD. Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform. Curr Opin Biotechnol 2014; 30:32-9. [DOI: 10.1016/j.copbio.2014.04.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 11/27/2022]
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Kelwick R, MacDonald JT, Webb AJ, Freemont P. Developments in the tools and methodologies of synthetic biology. Front Bioeng Biotechnol 2014; 2:60. [PMID: 25505788 PMCID: PMC4244866 DOI: 10.3389/fbioe.2014.00060] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/12/2014] [Indexed: 11/27/2022] Open
Abstract
Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a “body of knowledge” from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community.
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Affiliation(s)
- Richard Kelwick
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Medicine, Imperial College London , London , UK
| | - James T MacDonald
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Medicine, Imperial College London , London , UK
| | - Alexander J Webb
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Medicine, Imperial College London , London , UK
| | - Paul Freemont
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Medicine, Imperial College London , London , UK
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Si T, Xiao H, Zhao H. Rapid prototyping of microbial cell factories via genome-scale engineering. Biotechnol Adv 2014; 33:1420-32. [PMID: 25450192 DOI: 10.1016/j.biotechadv.2014.11.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/13/2014] [Accepted: 11/13/2014] [Indexed: 10/24/2022]
Abstract
Advances in reading, writing and editing genetic materials have greatly expanded our ability to reprogram biological systems at the resolution of a single nucleotide and on the scale of a whole genome. Such capacity has greatly accelerated the cycles of design, build and test to engineer microbes for efficient synthesis of fuels, chemicals and drugs. In this review, we summarize the emerging technologies that have been applied, or are potentially useful for genome-scale engineering in microbial systems. We will focus on the development of high-throughput methodologies, which may accelerate the prototyping of microbial cell factories.
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Affiliation(s)
- Tong Si
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Han Xiao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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Linshiz G, Stawski N, Goyal G, Bi C, Poust S, Sharma M, Mutalik V, Keasling JD, Hillson NJ. PR-PR: cross-platform laboratory automation system. ACS Synth Biol 2014; 3:515-24. [PMID: 25126893 DOI: 10.1021/sb4001728] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Golden Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms.
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Affiliation(s)
- Gregory Linshiz
- Fuels
Synthesis Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Physical
Bioscience Division, Lawrence Berkeley National Lab, 1 Cyclotron Road,
Mail Stop 978R4121, Berkeley, California 94720, United States
- DOE Joint Genome Institute, Walnut
Creek, California 94598, United States
| | - Nina Stawski
- Fuels
Synthesis Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Physical
Bioscience Division, Lawrence Berkeley National Lab, 1 Cyclotron Road,
Mail Stop 978R4121, Berkeley, California 94720, United States
| | - Garima Goyal
- Fuels
Synthesis Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Physical
Bioscience Division, Lawrence Berkeley National Lab, 1 Cyclotron Road,
Mail Stop 978R4121, Berkeley, California 94720, United States
| | - Changhao Bi
- Physical
Bioscience Division, Lawrence Berkeley National Lab, 1 Cyclotron Road,
Mail Stop 978R4121, Berkeley, California 94720, United States
- Tianjin
Institute of Industrial Biotechnology and Key Laboratory of Systems
Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Sean Poust
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Monica Sharma
- Physical
Bioscience Division, Lawrence Berkeley National Lab, 1 Cyclotron Road,
Mail Stop 978R4121, Berkeley, California 94720, United States
| | - Vivek Mutalik
- Physical
Bioscience Division, Lawrence Berkeley National Lab, 1 Cyclotron Road,
Mail Stop 978R4121, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Fuels
Synthesis Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Physical
Bioscience Division, Lawrence Berkeley National Lab, 1 Cyclotron Road,
Mail Stop 978R4121, Berkeley, California 94720, United States
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Nathan J. Hillson
- Fuels
Synthesis Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Physical
Bioscience Division, Lawrence Berkeley National Lab, 1 Cyclotron Road,
Mail Stop 978R4121, Berkeley, California 94720, United States
- DOE Joint Genome Institute, Walnut
Creek, California 94598, United States
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Blakes J, Raz O, Feige U, Bacardit J, Widera P, Ben-Yehezkel T, Shapiro E, Krasnogor N. Heuristic for maximizing DNA reuse in synthetic DNA library assembly. ACS Synth Biol 2014; 3:529-42. [PMID: 24730371 DOI: 10.1021/sb400161v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
De novo DNA synthesis is in need of new ideas for increasing production rate and reducing cost. DNA reuse in combinatorial library construction is one such idea. Here, we describe an algorithm for planning multistage assembly of DNA libraries with shared intermediates that greedily attempts to maximize DNA reuse, and show both theoretically and empirically that it runs in linear time. We compare solution quality and algorithmic performance to the best results reported for computing DNA assembly graphs, finding that our algorithm achieves solutions of equivalent quality but with dramatically shorter running times and substantially improved scalability. We also show that the related computational problem bounded-depth min-cost string production (BDMSP), which captures DNA library assembly operations with a simplified cost model, is NP-hard and APX-hard by reduction from vertex cover. The algorithm presented here provides solutions of near-minimal stages and thanks to almost instantaneous planning of DNA libraries it can be used as a metric of "manufacturability" to guide DNA library design. Rapid planning remains applicable even for DNA library sizes vastly exceeding today's biochemical assembly methods, future-proofing our method.
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35
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Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol 2014; 12:355-67. [DOI: 10.1038/nrmicro3240] [Citation(s) in RCA: 461] [Impact Index Per Article: 46.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Golberg A, Linshiz G, Kravets I, Stawski N, Hillson NJ, Yarmush ML, Marks RS, Konry T. Cloud-enabled microscopy and droplet microfluidic platform for specific detection of Escherichia coli in water. PLoS One 2014; 9:e86341. [PMID: 24475107 PMCID: PMC3903517 DOI: 10.1371/journal.pone.0086341] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 12/12/2013] [Indexed: 12/13/2022] Open
Abstract
We report an all-in-one platform – ScanDrop – for the rapid and specific capture, detection, and identification of bacteria in drinking water. The ScanDrop platform integrates droplet microfluidics, a portable imaging system, and cloud-based control software and data storage. The cloud-based control software and data storage enables robotic image acquisition, remote image processing, and rapid data sharing. These features form a “cloud” network for water quality monitoring. We have demonstrated the capability of ScanDrop to perform water quality monitoring via the detection of an indicator coliform bacterium, Escherichia coli, in drinking water contaminated with feces. Magnetic beads conjugated with antibodies to E. coli antigen were used to selectively capture and isolate specific bacteria from water samples. The bead-captured bacteria were co-encapsulated in pico-liter droplets with fluorescently-labeled anti-E. coli antibodies, and imaged with an automated custom designed fluorescence microscope. The entire water quality diagnostic process required 8 hours from sample collection to online-accessible results compared with 2–4 days for other currently available standard detection methods.
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Affiliation(s)
- Alexander Golberg
- Centre for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Shriners Burns Institute, Boston, Massachusetts, United States of America
| | - Gregory Linshiz
- Fuels Synthesis Division, Joint BioEnergy Institute, Emeryville, California, United States of America ; Physical BioSciences Division, Lawrence Berkeley National Labs, Berkeley, California, United States of America ; DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Ilia Kravets
- Department of Computer Science, Technion Institute of Technology, Haifa, Israel
| | - Nina Stawski
- Fuels Synthesis Division, Joint BioEnergy Institute, Emeryville, California, United States of America ; Physical BioSciences Division, Lawrence Berkeley National Labs, Berkeley, California, United States of America
| | - Nathan J Hillson
- Fuels Synthesis Division, Joint BioEnergy Institute, Emeryville, California, United States of America ; Physical BioSciences Division, Lawrence Berkeley National Labs, Berkeley, California, United States of America ; DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Martin L Yarmush
- Centre for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Shriners Burns Institute, Boston, Massachusetts, United States of America ; Department of Biomedical Engineering, Rutgers University, New Jersey, United States of America
| | - Robert S Marks
- Department of Biotechnology Engineering, The National Institute of Biotechnology in Negev, Ben Gurion University, Beer-Sheva, Israel ; School of Materials Science and Engineering, Nanyang Technological University, Singapore ; NRF CREATE program for Nanomaterials in Energy and Water Management, Singapore
| | - Tania Konry
- Department of Pharmaceutical Sciences, School of Pharmacy Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, United States of America
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Abstract
Modern standardized methodologies, described in detail in the previous chapters of this book, have enabled the software-automated design of optimized DNA construction protocols. This chapter describes how to design (combinatorial) scar-less DNA assembly protocols using the web-based software j5. j5 assists biomedical and biotechnological researchers construct DNA by automating the design of optimized protocols for flanking homology sequence as well as type IIS endonuclease-mediated DNA assembly methodologies. Unlike any other software tool available today, j5 designs scar-less combinatorial DNA assembly protocols, performs a cost-benefit analysis to identify which portions of an assembly process would be less expensive to outsource to a DNA synthesis service provider, and designs hierarchical DNA assembly strategies to mitigate anticipated poor assembly junction sequence performance. Software integrated with j5 add significant value to the j5 design process through graphical user-interface enhancement and downstream liquid-handling robotic laboratory automation.
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38
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Bi C, Su P, Müller J, Yeh YC, Chhabra SR, Beller HR, Singer SW, Hillson NJ. Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production. Microb Cell Fact 2013; 12:107. [PMID: 24219429 PMCID: PMC3831590 DOI: 10.1186/1475-2859-12-107] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 11/11/2013] [Indexed: 01/20/2023] Open
Abstract
Background The chemoautotrophic bacterium Ralstonia eutropha can utilize H2/CO2 for growth under aerobic conditions. While this microbial host has great potential to be engineered to produce desired compounds (beyond polyhydroxybutyrate) directly from CO2, little work has been done to develop genetic part libraries to enable such endeavors. Results We report the development of a toolbox for the metabolic engineering of Ralstonia eutropha H16. We have constructed a set of broad-host-range plasmids bearing a variety of origins of replication, promoters, 5’ mRNA stem-loop structures, and ribosomal binding sites. Specifically, we analyzed the origins of replication pCM62 (IncP), pBBR1, pKT (IncQ), and their variants. We tested the promoters PBAD, T7, Pxyls/PM, PlacUV5, and variants thereof for inducible expression. We also evaluated a T7 mRNA stem-loop structure sequence and compared a set of ribosomal binding site (RBS) sequences derived from Escherichia coli, R. eutropha, and a computational RBS design tool. Finally, we employed the toolbox to optimize hydrocarbon production in R. eutropha and demonstrated a 6-fold titer improvement using the appropriate combination of parts. Conclusion We constructed and evaluated a versatile synthetic biology toolbox for Ralstonia eutropha metabolic engineering that could apply to other microbial hosts as well.
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Affiliation(s)
| | | | | | | | - Swapnil R Chhabra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Cobb RE, Ning JC, Zhao H. DNA assembly techniques for next-generation combinatorial biosynthesis of natural products. J Ind Microbiol Biotechnol 2013; 41:469-77. [PMID: 24127070 DOI: 10.1007/s10295-013-1358-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/25/2013] [Indexed: 12/30/2022]
Abstract
Natural product scaffolds remain important leads for pharmaceutical development. However, transforming a natural product into a drug entity often requires derivatization to enhance the compound's therapeutic properties. A powerful method by which to perform this derivatization is combinatorial biosynthesis, the manipulation of the genes in the corresponding pathway to divert synthesis towards novel derivatives. While these manipulations have traditionally been carried out via restriction digestion/ligation-based cloning, the shortcomings of such techniques limit their throughput and thus the scope of corresponding combinatorial biosynthesis experiments. In the burgeoning field of synthetic biology, the demand for facile DNA assembly techniques has promoted the development of a host of novel DNA assembly strategies. Here we describe the advantages of these recently developed tools for rapid, efficient synthesis of large DNA constructs. We also discuss their potential to facilitate the simultaneous assembly of complete libraries of natural product biosynthetic pathways, ushering in the next generation of combinatorial biosynthesis.
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Affiliation(s)
- Ryan E Cobb
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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