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Revision as of 17:37, 16 October 2014
BBF RFC 105: Standardized Plant Syntax
Purpose
The difference in the biology of plants unveils a need for new standards. We decided to write a Request for Comments (RFC) to unite the plant SynBio community by defining a common language for plant synthetic biology, extensible to all other Eukaryotes. Its syntax is based on the Golden Gate System1 cloning method which uses TypeIIS restriction enzymes; variations, such as GB2.02 and MoClo3, are already being used across the field. This RFC brings together their common features and sets a consensus across the plant field for construct assembly and part repositories.
Marchantia polymorpha, a primitive liverwort, is being established as a new model organism for plant Synthetic Biology4; Contrary to historical model species, the choice of M. polymorpha has preceded its establishment. This is an opportunity to set standards in a coherent and united way paving the way for faster and more efficient sharing of information and parts.
The fewer the rules defining a standard, the more widely that standard is adopted. The introduction of this new chassis with its novel tool kit is the occasion to allow more flexibility in the Registry5, opening it to wider usage and contributions.
Thank you to the UEA and Valencia iGEM teams for their collaborations.
- Engler C, Youles M, Gruetzner R, Ehnert T-M, Werner S, et al. (2014) A golden gate modular cloning toolbox for plants. ACS Synth Biol: doi:10.1021/sb4001504.
- Sarrion-Perdigones A., Falconi E.E., Zandalinas S.I., Juarez P., Fernandez-del-Carmen A., Granell A., Orzaez D. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PLoS One 2011;6:e21622.
- Weber E., Engler C., Gruetzner R., Werner S., Marillonnet S. A modular cloning system for standardized assembly of multigene constructs. PLoS One 2011;6:e16765.
- http://synbio.org.uk/marchantia/
- http://parts.igem.org/Main_Page
Standardized Fusion Sequences
One part of the RFC was reaching a consensus on fusion sequences:
| Nature of Simplest Part | 5′ 4bp overhang | 3′ 4bp overhang |
|---|---|---|
| Pro = Promoter | GGAG | TACT |
| 5U = 5′ UTR up to atg | TACT | AATG |
| 5U(f) = 5′ UTR (for fusing to NT1 modules) | TACT | CCAT |
| NT1 = N-terminal tag/signal peptide | CCAT | AATG |
| NT2 = N-terminal tag/signal peptide | AATG | AGCC |
| CDS1 = Coding sequence | AATG | GCTT |
| CDS2 = Coding sequence (for fusing with SP) | AGCC | GCTT |
| CDS1ns = Coding sequence (no stop) (for fusing to CT modules) | AATG | TTCG |
| CDS2ns = Coding sequence (no stop) (for fusing with SP and CT modules) | AGCC | TTCG |
| CT = C-terminal tag/fusion protein | TTCG | GCTT |
| 3U= 3′ UTR | GCTT | GGTA |
| Ter= terminator | GGTA | CGCT |
| OP1 | GGAG | TGAC |
| OP2 | TGAC | TCCC |
| Mini Pro + 5U | TCCC | ATG |
