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

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.

Christian Rogers | Diego Orzaez | Antonio Granell | Jim Haseloff | Colette Matthewman | Anne Osbourn | Michael Udvardi | Alain Tissier | Sylvestre Marillonnet | Cyril Zipfel | Jonathan D. G. Jones | Jens Stougaard | Asaph Aharoni | Heiko Rischer | Jonathan D G Jones | Keith J Edwards | Nicola J Patron | Katherine Denby | Sophien Kamoun | Silke Robatzek | David C Baulcombe | Sebastian Schornack | Harro Bouwmeester | J. Ajioka | N. Patron | A. Osbourn | A. Webb | J. Langdale | D. Baulcombe | K. Edwards | K. Denby | B. Hamberger | C. Zipfel | A. Aharoni | S. Marillonnet | T. Brutnell | H. Bouwmeester | R. Field | Cathie Martin | P. Fraser | S. Schornack | P. Shih | S. Robatzek | D. Loqué | Jean-Michel Ané | D. Sanders | M. Udvardi | A. Granell | J. Stougaard | J. Haseloff | J. Hibberd | A. Breakspear | S. Kamoun | H. Kuhn | C. Raines | Alison M. Smith | C. Rogers | S. Fox | P. Schäfer | H. Rischer | G. Oldroyd | B. Wulff | D. Orzáez | Jonathan D. G. Jones | A. Webb | P. Delaux | A. Tissier | Patrick Schäfer | Thomas P Brutnell | H. Warzecha | C. Matthewman | Paul D Fraser | Dale Sanders | Heribert Warzecha | H. P. van Esse | Mark Youles | Oleg Raitskin | Aymeric Leveau | Gemma Farré | Alison Smith | Julian Hibberd | Alex A R Webb | James Locke | Jim Ajioka | Hannah Kuhn | H Peter Van Esse | Giles Oldroyd | Cathie Martin | Rob Field | Sarah O'Connor | Samantha Fox | Brande Wulff | Ben Miller | Andy Breakspear | Guru Radhakrishnan | Pierre-Marc Delaux | Dominique Loqué | Patrick Shih | W Paul Quick | Christine Raines | Paul F South | Jean-Michel Ané | Björn R Hamberger | Jane Langdale | James A H Murray | Vardis Ntoukakis | Paul F. South | Guru V. Radhakrishnan | W. P. Quick | O. Raitskin | A. Leveau | Sarah O'Connor | M. Youles | James A. H. Murray | J. Locke | P. South | Ben Miller | V. Ntoukakis | G. Farré | Sarah O’Connor | Hannah Kuhn | H. van Esse | Alison Smith

[1]  S. Elledge,et al.  SLIC: a method for sequence- and ligation-independent cloning. , 2012, Methods in molecular biology.

[2]  Wusheng Liu,et al.  Advanced genetic tools for plant biotechnology , 2013, Nature Reviews Genetics.

[3]  Jingdong Tian,et al.  Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways , 2009, PloS one.

[4]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[5]  Virginia Rutten,et al.  BBF RFC 106: A Standard Type IIS Syntax for Plants , 2015 .

[6]  Thomas F. Knight,et al.  Idempotent Vector Design for Standard Assembly of Biobricks , 2003 .

[7]  A. Granell,et al.  GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules , 2011, PloS one.

[8]  Carola Engler,et al.  A One Pot, One Step, Precision Cloning Method with High Throughput Capability , 2008, PloS one.

[9]  R. Edwards,et al.  Plant synthetic biology: a new platform for industrial biotechnology. , 2014, Journal of experimental botany.

[10]  J. Forment,et al.  GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology1[C][W][OA] , 2013, Plant Physiology.

[11]  Drew Endy,et al.  Engineering BioBrick vectors from BioBrick parts , 2008, Journal of Biological Engineering.

[12]  Nicola J. Patron,et al.  A golden gate modular cloning toolbox for plants. , 2014, ACS synthetic biology.

[13]  Carola Engler,et al.  Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes , 2009, PloS one.

[14]  M. Parniske,et al.  A Modular Plasmid Assembly Kit for Multigene Expression, Gene Silencing and Silencing Rescue in Plants , 2014, PloS one.

[15]  Jay D Keasling,et al.  BglBricks: A flexible standard for biological part assembly , 2010, Journal of biological engineering.

[16]  Sylvestre Marillonnet,et al.  Fast track assembly of multigene constructs using Golden Gate cloning and the MoClo system. , 2012, Bioengineered bugs.

[17]  Ira Phillips,et al.  A New Biobrick Assembly Strategy Designed for Facile Protein Engineering , 2006 .

[18]  Maxime Durot,et al.  Rapid and reliable DNA assembly via ligase cycling reaction. , 2014, ACS synthetic biology.

[19]  Nicola J Patron,et al.  DNA assembly for plant biology: techniques and tools. , 2014, Current opinion in plant biology.

[20]  J. Dinneny,et al.  A robust family of Golden Gate Agrobacterium vectors for plant synthetic biology , 2013, Front. Plant Sci..

[21]  J. Lohmann,et al.  GreenGate - A Novel, Versatile, and Efficient Cloning System for Plant Transgenesis , 2013, PloS one.

[22]  Tom Ellis,et al.  DNA assembly for synthetic biology: from parts to pathways and beyond. , 2011, Integrative biology : quantitative biosciences from nano to macro.

[23]  Ernst Weber,et al.  A Modular Cloning System for Standardized Assembly of Multigene Constructs , 2011, PloS one.

[24]  Wusheng Liu,et al.  Advanced genetic tools for plant biotechnology , 2013, Nature Reviews Genetics.

[25]  G. Braus,et al.  Establishing a versatile Golden Gate cloning system for genetic engineering in fungi. , 2014, Fungal genetics and biology : FG & B.

[26]  H. Warzecha,et al.  A Modular Cloning Toolbox for the Generation of Chloroplast Transformation Vectors , 2014, PloS one.