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      Standards for plant synthetic biology: a common syntax for exchange of DNA parts

      Author(s): 1 , 2 , 3 , 4 , 5 , 2 , 6 , 1 , 1 , 2 , 6 , 6 , 6 , 2 , 7 , 2 , 7 , 2 , 7 , 2 , 8 , 2 , 8 , 2 , 9 , 2 , 7 , 1 , 1 , 1 , 1 , 1 ,   1 , 2 , 6 , 2 , 6 , 2 , 6 , 2 , 6 , 2 , 6 , 6 , 6 , 6 , 6 , 6 , 6 , 10 , 11 , 3 , 4 , 10 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 26 , 26 , 27 , 2 , 6 , 2 , 7
      Publication date (Electronic):
      Journal: New Phytologist
      Publisher: Wiley

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          Abstract

          Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.

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          Enzymatic assembly of DNA molecules up to several hundred kilobases.

          Daniel Gibson, Lei Young, Ray-Yuan Chuang … (2009)
          We describe an isothermal, single-reaction method for assembling multiple overlapping DNA molecules by the concerted action of a 5' exonuclease, a DNA polymerase and a DNA ligase. First we recessed DNA fragments, yielding single-stranded DNA overhangs that specifically annealed, and then covalently joined them. This assembly method can be used to seamlessly construct synthetic and natural genes, genetic pathways and entire genomes, and could be a useful molecular engineering tool.
          Article 0 comments Cited 1844 times – based on 0 reviews     Review now
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            A One Pot, One Step, Precision Cloning Method with High Throughput Capability

            Carola Engler, Romy Kandzia, Sylvestre Marillonnet (2008)
            Current cloning technologies based on site-specific recombination are efficient, simple to use, and flexible, but have the drawback of leaving recombination site sequences in the final construct, adding an extra 8 to 13 amino acids to the expressed protein. We have devised a simple and rapid subcloning strategy to transfer any DNA fragment of interest from an entry clone into an expression vector, without this shortcoming. The strategy is based on the use of type IIs restriction enzymes, which cut outside of their recognition sequence. With proper design of the cleavage sites, two fragments cut by type IIs restriction enzymes can be ligated into a product lacking the original restriction site. Based on this property, a cloning strategy called ‘Golden Gate’ cloning was devised that allows to obtain in one tube and one step close to one hundred percent correct recombinant plasmids after just a 5 minute restriction-ligation. This method is therefore as efficient as currently used recombination-based cloning technologies but yields recombinant plasmids that do not contain unwanted sequences in the final construct, thus providing precision for this fundamental process of genetic manipulation.
            Article 0 comments Cited 415 times – based on 0 reviews     Review now
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              Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes

              Carola Engler, Ramona Gruetzner, Romy Kandzia … (2009)
              We have developed a protocol to assemble in one step and one tube at least nine separate DNA fragments together into an acceptor vector, with 90% of recombinant clones obtained containing the desired construct. This protocol is based on the use of type IIs restriction enzymes and is performed by simply subjecting a mix of 10 undigested input plasmids (nine insert plasmids and the acceptor vector) to a restriction-ligation and transforming the resulting mix in competent cells. The efficiency of this protocol allows generating libraries of recombinant genes by combining in one reaction several fragment sets prepared from different parental templates. As an example, we have applied this strategy for shuffling of trypsinogen from three parental templates (bovine cationic trypsinogen, bovine anionic trypsinogen and human cationic trypsinogen) each divided in 9 separate modules. We show that one round of shuffling using the 27 trypsinogen entry plasmids can easily produce the 19,683 different possible combinations in one single restriction-ligation and that expression screening of a subset of the library allows identification of variants that can lead to higher expression levels of trypsin activity. This protocol, that we call ‘Golden Gate shuffling’, is robust, simple and efficient, can be performed with templates that have no homology, and can be combined with other shuffling protocols in order to introduce any variation in any part of a given gene.
              Article 0 comments Cited 388 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Title: New Phytologist
                Abbreviated Title: New Phytol
                Publisher: Wiley
                ISSN (Print): 0028-646X
                ISSN (Electronic): 1469-8137
                Publication date Created: October 2015
                Publication date (Electronic): July 14 2015
                Publication date (Print): October 2015
                Volume: 208
                Issue: 1
                Pages: 13-19
                Affiliations
                [1 ]The Sainsbury Laboratory Norwich Research Park Norwich, NR4 7RG UK
                [2 ]OpenPlant Consortium: The University of Cambridge The John Innes Centre and The Sainsbury Laboratory Norwich NR4 7UH UK
                [3 ]Instituto de Biología Molecular y Celular de Plantas (IBMCP) Consejo Superior de Investigaciones Científicas Universidad Politécnica de Valencia Avda Tarongers SN Valencia Spain
                [4 ]Leibniz‐Institut für Pflanzenbiochemie Weinberg 3 06120 Halle (Saale) Germany
                [5 ]Plant Biotechnology and Metabolic Engineering Technische Universität Darmstadt Schnittspahnstrasse 4 Darmstadt 64287 Germany
                [6 ]The John Innes Centre Norwich Research Park Norwich NR4 7UH UK
                [7 ]Department of Plant Sciences University of Cambridge Downing Street Cambridge, CB2 3EA UK
                [8 ]The Sainsbury Laboratory Cambridge University Bateman Street Cambridge, CB2 1LR UK
                [9 ]Department of Pathology University of Cambridge Tennis Court Road Cambridge, CB2 1QP UK
                [10 ]Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
                [11 ]Joint BioEnergy Institute EmeryStation East 5885 Hollis St, 4th Floor Emeryville CA 94608 USA
                [12 ]The Donald Danforth Plant Science Center St Louis MO 63132 USA
                [13 ]Department of Animal and Plant Sciences University of Sheffield Sheffield S10 2TN, UK
                [14 ]VTT Technical Research Centre of Finland Espoo 02044 Finland
                [15 ]School of Biological Sciences Royal Holloway University of London Egham Hill Egham TW20 0EX UK
                [16 ]Department of Plant Sciences Weizmann Institute of Science Rehovot 76100 Israel
                [17 ]School of Biological Sciences University of Essex Colchester CO4 3SQ, UK
                [18 ]United States Department of Agriculture Global Change and Photosynthesis Research Unit ARS 1206 West Gregory Drive Urbana IL 61801 USA
                [19 ]Departments of Bacteriology and Agronomy University of Wisconsin 1575 Linden Drive Madison WI 53706 USA
                [20 ]Biochemistry Laboratory Department of Plant and Environmental Sciences University of Copenhagen Thorvaldsensvej 40 Frederiksberg C Denmark
                [21 ]Department of Plant Sciences University of Oxford Oxford, OX1 3RB UK
                [22 ]Centre for Carbohydrate Recognition and Signalling Department of Molecular Biology and Genetics Aarhus University Gustav Wieds Vej 10C Aarhus Denmark
                [23 ]Wageningen UR Wageningen University Wageningen 6700 AA the Netherlands
                [24 ]Plant Biology Division The Samuel Roberts Noble Foundation 2510 Sam Noble Parkway Ardmore OK 73401 USA
                [25 ]School of Biosciences Sir Martin Evans Building Cardiff University Museum Avenue Cardiff, CF10 3AX UK
                [26 ]Warwick Integrative Synthetic Biology Centre and School of Life Sciences University of Warwick Coventry, CV4 7AL UK
                [27 ]BrisSynBio Life Sciences Building University of Bristol Tyndall Avenue Bristol, BS8 1TQ UK
                Article
                DOI: 10.1111/nph.13532
                PubMed ID: 26171760
                SO-VID: 43248e48-8ee4-4a00-a329-fe550f63da61
                Copyright © © 2015
                License:

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                http://doi.wiley.com/10.1002/tdm_license_1.1

                http://doi.wiley.com/10.1002/tdm_license_1.1

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