• Research

Development and application of standards for plant synthetic biology

Biological assembly standards for the facilitation, automation and streamlining of synthetic biology projects in plant systems.

Project summary.

Led by: Patron Group

Start date: 31 July 2014

End date: 2 September 2019

Duration: 61 months

Grants:

BBSRC Synthetic Biology Research Centre ‘OpenPlant’ Award (BB/L014130/1)

BBR Targeted gene knockouts in crops using RNA-guided Cas9 nuclease BB/N019466/1

Funding:

Total award £11,787,968

EI amount £400,000

With their ability to directly utilize CO2 and sunlight to produce a diverse range of organic compounds, plants and algae are attractive chassis bioengineering. Synthetic biology offers the means and opportunity to engineer plants and algae for new roles in our environment, to produce therapeutic compounds and to address global problems such as food insecurity and the contamination of ecosystems with agrochemicals and macronutrients.

The ability to program cells by providing new instructions written in DNA is a foundational technology of the field, however, for many years the assembly of DNA circuits was laborious and unreliable. In other engineering fields, standardisation of components has driven speed of innovation and the economy of production; components can be selected from libraries and catalogues of standard parts in which specifications and performance characteristics

are described. This conceptual model is the basis of synthetic biology, with the same ideal being applied to biological parts (DNA fragments).  Biological assembly standards allow DNA parts, even those from multiple laboratories and experiments, to be assembled together using the same reagents and protocols. The adoption of such standards for bioengineering in plants has been cohesive for the plant science community.

To address the lack of interoperability and the consequential replication of efforts produced by parallel adoption of different standards, we led the establishment of a common genetic syntax for the exchange of DNA parts for Type IIS mediated assembly. We are now applying this standard to the application of genome-scale engineering. It is also underpinning the automation of DNA assembly at nanoscales in the DNA Foundry.

Details.

Plant scientists rapidly adopted technologies based on Type IIS restriction enzymes, known widely as ‘Golden Gate’. One of the key benefits of Type IIS-mediated assembly is that it can be modularized to allow the production of standard parts that can be assembled together in the desired order simply by mixing the intact plasmids housing the parts together with an acceptor plasmid and an enzyme cocktail. This reaction is fully automatable, an advantage over other methods that require amplification and purification of fragments.

However, as Type IIS methods spread and gained popularity in the community, the interoperability of basic parts was lost as individual laboratories varied and extended the modules outlined in the first publications. By 2014, six years after the original publication, several consortia of plant scientists had adopted shared standards but were unable to interface with those outside of their syndicates and a number of labs were using entirely bespoke systems.

To address the lack of interoperability and the consequential replication of efforts to produce parts compatible each different standard, we consulted with the community and established a ratified common genetic syntax for the exchange of DNA parts for plant synthetic biology. This defined twelve fusion sites at the boundaries of the functional elements that comprise a eukaryotic gene as well as describing the features of the plasmids that house standard parts. We are now applying this standard to the application of genome-scale engineering including CAS9-mediated genome engineering. The standard is also being automated in the DNA Foundry.

Tools.

The Universal Acceptor for cloning new parts in the Plant Common Syntax

This plasmid can be used to make new standard parts compatible with the common syntax.

pUAP1 AddGene #63674

Publications.

Blueprints for green biotech: development and application of standards for plant synthetic biology

Patron, N.J., Biochemical Society Transactions 44, 702-708 (2016)
DOI: 10.1042/BST20160044

Standards for Plant Synthetic Biology: A Common Syntax for Exchange of DNA Parts

Patron, N.J. et al., New Phytologist 208,13-9 (2015)
DOI: 10.1111/nph.13532

BBF RFC 106: A Standard Type IIS Syntax for Plants

Rutten, V. et al. (2015)

Collaborators.

The OpenPlant Consortium

OpenPlant is a collaborative initiative between the University of Cambridge, the John Innes Centre and the Sainsbury Laboratory in Norwich. The initiative promotes interdisciplinary exchange, open technologies for innovation and responsible innovation for sustainable agriculture and conservation. The Development and application of standards for plant synthetic biology was a collaborative aim of the consortium to underpin the efforts in all work-packages.

Impact statement.

The establishment of a ratified standard for DNA assembly for plant synthetic biology has been cohesive for the plant science community, facilitating the application of genome editing technologies to plant systems and streamlining progress in large-scale, multi-laboratory bioengineering projects. It was featured in the UK Synthetic Biology Strategic Plan 2016: BioDesign for the Bioeconomy.