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

New Phytologist

Volumn 208, Issue 1, 2015, Pages 13-19

  Patron, Nicola J ^a,b   Orzaez, Diego ^c   Marillonnet, Sylvestre ^d   Warzecha, Heribert ^e   Matthewman, Colette ^b,f   Youles, Mark ^a   Raitskin, Oleg ^a,b   Leveau, Aymeric ^f   Farré, Gemma ^f   Rogers, Christian ^f   Smith, Alison ^b   Hibberd, Julian ^b   Webb, Alex A R ^b   Locke, James ^b,g   Schornack, Sebastian ^b,g   Ajioka, Jim ^b   Baulcombe, David C ^b   Zipfel, Cyril ^a   Kamoun, Sophien ^a   Jones, Jonathan D G ^a   Kuhn, Hannah ^a   Robatzek, Silke ^a   Van Esse, H Peter ^a   Sanders, Dale ^b,f   Oldroyd, Giles ^b,f   Martin, Cathie ^b,f   Field, Rob ^b,f   O'Connor, Sarah ^b,f   Fox, Samantha ^f   Wulff, Brande ^f   Miller, Ben ^f   Breakspear, Andy ^f   Radhakrishnan, Guru ^f   Delaux, Pierre Marc ^f   Loqué, Dominique ^h,i   Granell, Antonio ^c   Tissier, Alain ^d   Shih, Patrick ^h   Brutnell, Thomas P ^j   Quick, W Paul ^k   Rischer, Heiko ^l   Fraser, Paul D ^m   Aharoni, Asaph ⁿ   Raines, Christine ^o   South, Paul F ^p   Ané, Jean Michel ^q   Hamberger, Björn R ^r   Langdale, Jane ^s   Stougaard, Jens ^t   Bouwmeester, Harro ^u   Udvardi, Michael ^v   Murray, James A H ^w   Ntoukakis, Vardis ^x   Schäfer, Patrick ^x   Denby, Katherine ^x   Edwards, Keith J ^y   Osbourn, Anne ^b,f   Haseloff, Jim ^b   more..

^a NORWICH RESEARCH PARK   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITAT POLITÈCNICA DE VALÈNCIA   (Spain)

^d LEIBNIZ INSTITUTE OF PLANT BIOCHEMISTRY   (Germany)

^e DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

^f JOHN INNES CENTRE   (United Kingdom)

^g UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^h LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

ⁱ JOINT BIOENERGY INSTITUTE   (United States)

^j DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

^k UNIVERSITY OF SHEFFIELD   (United Kingdom)

^l VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

^m UNIVERSITY OF LONDON   (United Kingdom)

ⁿ WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^o UNIVERSITY OF ESSEX   (United Kingdom)

^p U S DEPARTMENT OF AGRICULTURE   (United States)

^q UNIVERSITY OF WISCONSIN MADISON   (United States)

^r UNIVERSITY OF COPENHAGEN   (Denmark)

^s UNIVERSITY OF OXFORD   (United Kingdom)

^t AARHUS UNIVERSITY   (Denmark)

^u WAGENINGEN UNIVERSITY   (Netherlands)

^v PLANT BIOLOGY DIVISION   (United States)

^w CARDIFF UNIVERSITY   (United Kingdom)

^x UNIVERSITY OF WARWICK   (United Kingdom)

^y Tankard's Close   (United Kingdom)

more..

Author keywords

Cloning; DNA assembly; Genetic syntax; GoldenGate; Synthetic biology; Type IIS restriction endonucleases

Indexed keywords

CLONE; DEVELOPMENTAL BIOLOGY; DNA; ENZYME ACTIVITY; GENETIC ANALYSIS; PLANT COMMUNITY; SYNTAXONOMY;

EUKARYOTA;

DNA; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

BOTANY; EUKARYOTE; GENETIC ENGINEERING; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR CLONING; PLANT; PLASMID; PROCEDURES; STANDARD; STANDARDS; SYNTHETIC BIOLOGY; TRANSGENIC PLANT;

BOTANY; CLONING, MOLECULAR; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA; EUKARYOTA; GENETIC ENGINEERING; PLANTS; PLANTS, GENETICALLY MODIFIED; PLASMIDS; REFERENCE STANDARDS; SYNTHETIC BIOLOGY; TRANSCRIPTION, GENETIC;

EID: 84939807175     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/nph.13532     Document Type: Article

References (27)

1. Anderson JC, Dueber JE, Leguia M, Wu GC, Goler JA, Arkin AP, Keasling JD. 2010. BglBricks: a flexible standard for biological part assembly. Journal of Biological Engineering 4: e88218.
2. Binder A, Lambert J, Morbitzer R, Popp C, Ott T, Lahaye T, Parniske M. 2014. A modular plasmid assembly kit for multigene expression, gene silencing and silencing rescue in plants. PLoS ONE 9: e88218.
3. Cook C, Bastow R, Martin L. 2014. Developing plant synthetic biology in the UK - challenges and opportunities. Report from the 2013 GARNet meeting 'An introduction to opportunities in plant synthetic biology'. Cardiff, UK: GarNET.
4. Ellis T, Adie T, Baldwin GS. 2011. DNA assembly for synthetic biology: from parts to pathways and beyond. Integrative Biology 3: 109-118.
5. Emami S, Yee M-C, Dinneny JR. 2013. A robust family of Golden Gate Agrobacterium vectors for plant synthetic biology. Frontiers in Plant Science 4: 339.
6. Engler C, Gruetzner R, Kandzia R, Marillonnet S. 2009. Golden Gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS ONE 4: e5553.
7. Engler C, Kandzia R, Marillonnet S. 2008. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3: e3647.
8. Engler C, Youles M, Grüetzner R, Ehnert T-M, Werner S, Jones JDG, Patron NJ, Marillonnet S. 2014. A Golden Gate modular cloning toolbox for plants. ACS Synthetic Biology 3: 839-843.
9. Fesenko E, Edwards R. 2014. Plant synthetic biology: a new platform for industrial biotechnology. Journal of Experimental Botany 65: 1927-1937.
10. Gibson D, Young L, Chuang R, Venter C, Hutchison CA III, Smith H. 2009. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature Methods 6: 343-345.
11. Knight T. 2003. Idempotent vector design for standard assembly of BioBricks. Boston, MA, USA: MIT Synthetic Biology Working Group, MIT Artificial Intelligence Laboratory.
12. Kok S, Stanton L, Slaby T. 2014. Rapid and reliable DNA assembly via ligase cycling reaction. ACS Synthetic Biology 3: 97-106.
13. Lampropoulos A, Sutikovic Z, Wenzl C, Maegele I, Lohmann JU, Forner J. 2013. GreenGate - a novel, versatile, and efficient cloning system for plant transgenesis. PLoS ONE 8: e83043.
14. Li MZ, Elledge SJ. 2012. SLIC: a method for sequence- and ligation-independent cloning. In: Peccoud J, ed. Methods in molecular biology. Totowa, NJ, USA: Humana Press, 51-59.
15. Liu W, Yuan JS, Stewart CN. 2013. Advanced genetic tools for plant biotechnology. Nature Reviews Genetics 14: 781-793.
16. Patron NJ. 2014. DNA assembly for plant biology: techniques and tools. Current Opinion in Plant Biology 19C: 14-19.
17. Phillips I, Silver P. 2006. BBF RFC 23: a new BioBrick assembly strategy designed for facile protein engineering. [WWW document] URL http://hdl.handle.net/1721.1/32535 [accessed 16 June 2015].
18. Quan J, Tian J. 2009. Circular polymerase extension cloning of complex gene libraries and pathways. PLoS ONE 4: e6441.
19. Rutten V, Munabi A, Riche F, Lewy G, Wilson H, Pipan M, Bhate S, Nghiem T-A, Kaufhold W. 2015. BBF RFC 106: a standard Type IIS syntax for plants. [WWW document] URL http://hdl.handle.net/1721.1/96069 [accessed 16 June 2015].
20. Sarrion-Perdigones A, Falconi EE, Zandalinas SI, Juárez P, Fernández-del-Carmen A, Granell A, Orzaez D. 2011. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PLoS ONE 6: e21622.
21. Sarrion-Perdigones A, Vazquez-Vilar M, Palací J, Castelijns B, Forment J, Ziarsolo P, Blanca J, Granell A, Orzaez D. 2013. GoldenBraid2.0: a comprehensive DNA assembly framework for plant synthetic biology. Plant Physiology. 62: 1618-1631.
22. Shetty RP, Endy D, Knight TF. 2008. Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering 2: 5.
23. Terfrüchte M, Joehnk B, Fajardo-Somera R, Braus GH, Riquelme M, Schipper K, Feldbrügge M. 2014. Establishing a versatile Golden Gate cloning system for genetic engineering in fungi. Fungal Genetics and Biology 62: 1-10.
24. Vafaee Y, Staniek A, Mancheno-Solano M, Warzecha H. 2014. A modular cloning toolbox for the generation of chloroplast transformation vectors. PLoS ONE 9: e110222.
25. Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S. 2011. A modular cloning system for standardized assembly of multigene constructs. PLoS ONE 6: e16765.
26. Werner S, Engler C, Weber E, Gruetzner R, Marillonnet S. 2012. Fast track assembly of multigene constructs using Golden Gate cloning and the MoClo system. Bioengineered Bugs 3: 38-43.
27. ™. Genetic Engineering and Biotechnology News 76: 42.