First common standard for assembly of DNA parts in plant SynBio published

Dr Nicola Patron

Supported by OpenPlant, Dr Nicola Patron of The Sainsbury Laboratory, Norwich, has led development of the first common standard for the assembly of DNA parts for plant synthetic biology.

Published today in New Phytologist as a Viewpoint article, this standard has been agreed between the inventors and developers of several Type IIS cloning technologies, the leaders of numerous plant bioengineering consortia and leaders of international plant science.

In the article, Nicola and her co-authors describe a common syntax of twelve fusion sites to enable the facile assembly of eukaryotic transcriptional units.

The manuscript received favourable support in the peer review process. One reviewer commented that “ …this is somewhat of a landmark publication that will massively influence all plant synthetic biology to come and shows the community in this field to be ahead of their colleagues in other areas.” Another remarked that “this paper will be a catalyst for further discussion around standardization not only in plants but in synthetic biology in general.”

By establishing a standard for the wider plant community Nicola and her colleagues will facilitate the sharing of standard parts for plants between scientists. It also sets a basis for the development of software and hardware that will support accelerated design and automated assembly. Their vision is to develop an extensive catalogue of standardised, characterised DNA parts to accelerate plant bioengineering.

The establishment of a DNA assembly standard for plants is an important and timely step in plant synthetic biology.

Dr Jim Haseloff at the University of Cambridge said: “The publication of a common syntax for plant DNA parts is a landmark for the adoption of engineering principles in multicellular organisms. It is the result of wide cooperation between researchers across the plant biology field, and sets the scene for greater scientific exchange and innovation in crop improvement.”

Read the paper: ‘Standards for plant synthetic biology: a common syntax for exchange of DNA parts’

Edited from the post Dr Nicola Patron establishes first common standard for assembly of DNA parts in plant SynBio which appeared first on The Sainsbury Laboratory.

Source: Dr Nicola Patron establishes first common standard for assembly of DNA parts in plant SynBio

SynBioBeta post on OpenPlant: Open Technologies for Plant Synthetic Biology

Reposted from the SynBioBeta Blog

Plant synthetic biology has great potential to improve sustainable bioproduction of globally important products; from foodstuffs to fibres to drugs. Advantages of plants over engineered microbes include their worldwide cultivation, their harvest on a giga-tonne scale and the existing precedent for genetically modified crops in many parts of the world. In addition to these applied benefits, plants raise interesting scientific questions and technical challenges around engineering pathways and interactions in multi-cellular, differentiating and developing organisms, adding complexity to current microbial experiments.

Plant synthetic biology is a young field and requires the development of tools and techniques to deal with additional complexity, such as improved genome editing, DNA synthesis and assembly at chromosomal or genomic scales. Supply of plant DNA parts is expected to increase rapidly, which is why the sharing and characterization of these components is a priority; particularly in the liverwort Marchantia, which appears to be a promising candidate for a plant synthetic biology model organism. Tools identified as necessary to support these developments include hardware and software for automation of high-throughput assembly and characterization, plant-relevant software models, data repositories and standards to increase interoperability of the parts and their associated data.

Right: Image of Marchantia

The OpenPlant initiative is a BBSRC-EPSRC funded synthetic biology centre, based at the University of Cambridge, the John Innes Centre and The Sainsbury Laboratory in Norwich, that aims to address these foundational requirements and then apply them to engineer traits including plant metabolic pathways and natural product synthesis routes. Applications include input to major programmes addressing grand challenges for energy and food security. For example, carbohydrate engineering for improved yield of biofuels or studying Marchantia to inform a synthetic approach to nitrogen-fixing in cereals, where it could have major implications for fertilizer use. Metabolic diversity in plants supplies us with important drugs, flavorings and agrochemicals in addition to impacting plant ecology and protection, so another OpenPlant project concerns optimizing enzymes and engineering gene clusters to synthesize these compounds.

OpenPlant aims to shape working practices and norms in these early stages of plant synthetic biology, by promoting interdisciplinary exchange, the development of standards and responsible innovation. It promotes an ecosystem of open technologies giving researchers and small companies greater freedom to operate within a two-tier IP system. IP-free circulation of foundational tools and DNA parts should accelerate uptake, innovation and entrepreneurship; allowing exploration of new models for decentralized ownership, control and manufacture of synthetic plant technologies. Protecting inventions representing novel combinations and applications of these low-level components preserves investment and retains commercial prospects, while also promoting alternative business models.

Innovation in plant biotechnology, particularly in high-value areas such as crops, is increasingly constrained by intellectual property (IP) protection, sometimes restricting access to genetic tools. This can impede the ability of innovative synthetic biology programmes to succeed. Commercial entities from entrepreneurial startups to large multinationals already struggle through patent thickets when bringing products to market and both academic-industrial exchange and sharing among researchers is restricted by terms and conditions in materials transfer agreements. OpenPlant experiments with openness as a means to aid innovation, particularly as the scale of DNA systems increases and the number of parts and tools involved in creating an engineered organism grows. Openness also offers greater access to research tools for the development of synthetic plant products that have implications for global sustainability and international development, and that may rely on decentralized projects to address local needs.

These efforts are part of a broader ongoing exploration of open practices and commons-based knowledge production among many communities. Open source strategies have proved fruitful in software and computing, from multimillion dollar commercial companies such as RedHat built on the basis of openly distributed code, through to projects such as the Raspberry Pi and its associated open software interfaces, which are wildly popular among educators and makers, including scientists. CERN, a scientific organisation with a strong history of successful technology transfer, heavily promotes open source hardware projects. Their repository hosts over 100 projects, with 16 companies actively engaged in testing or producing hardware based on technologies developed at CERN.

Open research practices have been promoted at the grassroots of several academic communities and are fast becoming a focus of funding agencies hoping to leverage their potential for accelerating research and innovation and reducing inequities in access to knowledge. One project employing an approach analogous to OpenPlant is the Structural Genomics Consortium, a public-private partnership for drug discovery that restricts IP protection of any results until the later stages of clinical trials, thus moving the pre-competitive boundary later in the discovery pipeline. As per a recent evaluation report, its open access approach is considered a significant incentive for investment by commercial partners owing to better facilitation of downstream research and increased competitiveness further down the value chain. The benefits of sharing were felt by the companies involved to outweigh any risks and associated with late-stage IP protection.  Other projects such as Open Source Malaria have also described how open approaches accelerated their research, including via industrial partnerships.

In summary, OpenPlant is performing cutting edge synthetic biology research while also exploring the potential of open technologies by engaging with diverse partners, building communities and providing incentives for open projects, such as seed funding. We will document and share what we learn from our approach to promoting innovation and entrepreneurship alongside the technologies and scientific results arising from our research. We welcome feedback from the SynBioBeta community!