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

Nicola J Patron^{1

2}, Diego Orzaez³, Sylvestre Marillonnet⁴, Heribert Warzecha⁵, Colette Matthewman^{2

6}, Mark Youles¹, Oleg Raitskin^{1

2}, Aymeric Leveau⁶, Gemma Farré⁶, Christian Rogers⁶, Alison Smith^{2

7}, Julian Hibberd^{2

7}, Alex A R Webb^{2

7}, James Locke^{2

8}, Sebastian Schornack^{2

8}, Jim Ajioka^{2

9}, David C Baulcombe^{2

7}, Cyril Zipfel¹, Sophien Kamoun¹, Jonathan D G Jones¹, Hannah Kuhn¹, Silke Robatzek¹, H Peter Van Esse¹, Dale Sanders^{2

6}, Giles Oldroyd^{2

6}, Cathie Martin^{2

6}, Rob Field^{2

6}, Sarah O'Connor^{2

6}, Samantha Fox⁶, Brande Wulff⁶, Ben Miller⁶, Andy Breakspear⁶, Guru Radhakrishnan⁶, Pierre-Marc Delaux⁶, Dominique Loqué^{10

11}, Antonio Granell³, Alain Tissier⁴, Patrick Shih¹⁰, Thomas P Brutnell¹², W Paul Quick¹³, Heiko Rischer¹⁴, Paul D Fraser¹⁵, Asaph Aharoni¹⁶, Christine Raines¹⁷, Paul F South¹⁸, Jean-Michel Ané¹⁹, Björn R Hamberger²⁰, Jane Langdale²¹, Jens Stougaard²², Harro Bouwmeester²³, Michael Udvardi²⁴, James A H Murray²⁵, Vardis Ntoukakis²⁶, Patrick Schäfer²⁶, Katherine Denby²⁶, Keith J Edwards²⁷, Anne Osbourn^{2

6}, Jim Haseloff^{2

7}

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.

PMID: 26171760
DOI: 10.1111/nph.13532

Free article

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

Nicola J Patron et al. New Phytol. 2015 Oct.

Free article

. 2015 Oct;208(1):13-9.

doi: 10.1111/nph.13532. Epub 2015 Jul 14.

Authors

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.

PMID: 26171760
DOI: 10.1111/nph.13532

Erratum in

Corrigendum. Standards for plant synthetic biology: a common syntax for exchanges of DNA parts.
Patron NJ, Orzaez O, Marillonnet S, Warzecha H, Matthewman C, Youles M, Raitskin O, Leveau A, Farré G, Rogers C. Patron NJ, et al. New Phytol. 2016 Jan;209(2):885. doi: 10.1111/nph.13773. Epub 2015 Nov 12. New Phytol. 2016. PMID: 26763681 No abstract available.

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.

Keywords: DNA assembly; GoldenGate; Type IIS restriction endonucleases; cloning; genetic syntax; synthetic biology.

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

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

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