An introduction to synthetic biology in plant systems: ERASynBio/OpenPlant summer school for early career researchers, September 2014.

Abstract

‘… an invaluable and enjoyable opportunity for early career researchers to learn from and engage with world-leading experts in plant synthetic biology.’ Plant synthetic biology is a burgeoning field that is attracting attention from both the synthetic biology and plant science communities (Osbourn et al., 2012; Cook et al., 2014), as illustrated by the recent funding of OpenPlant by the UK government through the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering and Physical Sciences Research Council (EPSRC), to develop foundational technologies for plant synthetic biology. The development of this new field is in part due to rapid technological advances allowing quick, easy and efficient manipulation of genomic and transgenic plant DNA, and therefore the summer school mainly focussed on these cutting-edge tools and applications, with the aim of encouraging their use by up-and-coming researchers. The 20 summer school participants had a variety of research backgrounds and levels of experience, from theorists and computer scientists to molecular, plant and synthetic biologists, and from new PhD students to postdoctoral researchers. Some of the participants had no previous plant science knowledge, so the major challenge was to devise a programme that would be engaging and instructive. As a result, participants were trained through a diverse course of lectures, practical sessions and group projects, covering a wide range of theoretical, technical and ethical content in this expanding discipline. The lecture programme was designed to teach the participants about synthetic biology concepts and new technologies both in theory and application, as well as introducing them to several model plant systems. In addition, technical talks provided practical details including plant transformation, bioinformatics and metabolite analysis. Discussion was encouraged following the talks, with participants taking the opportunity to meet and question world-leading experts. Claes Gustafsson, from the San Francisco-based DNA synthesis company DNA2.0, set the scene by introducing the theory behind the application of engineering values to synthetic biology, including the experimental cycle of designing, building, testing and learning that underpins effective synthetic biology research. Consistent with recent developments in plant synthetic biology, DNA assembly and genome engineering techniques were at the forefront of the more technical talks, and, importantly, illustrated with recent applications. Golden Gate cloning, a newly developed technique for assembling multigene DNA constructs in a modular fashion, was highlighted by several speakers, including Aymeric Leveau (Osbourn Laboratory, John Innes Centre, UK), who discussed its use in his work in metabolic engineering of wheat, whilst Samantha Fox (Coen laboratory, John Innes Centre, UK) explained how she had used Golden Gate cloning to develop a modular Cre-Lox system for inducible expression of a gene of interest in Arabidopsis thaliana. The talks were compiled to introduce the participants to cutting-edge methodologies driving the development of the plant synthetic biology field – notably, Diego Orzaez (Technical University of Valencia, Spain) outlined the GoldenBraid cloning system he has developed, based on Golden Gate, for iterative modular DNA assembly for plant biotechnology applications (Sarrion-Perdigones et al., 2011), and Jim Haseloff (University of Cambridge/OpenPlant, UK) promoted the simple liverwort plant Marchantia polymorpha as a new, tractable model system for plant synthetic biology. Genome editing in plants was also emphasized in the lectures as an increasingly invaluable and widespread synthetic biology tool, due to its relatively straightforward and efficient application. Sebastian Schornack (University of Cambridge, UK) described how the code for recognition of target DNA by TAL effectors was discovered (Boch et al., 2009) and how TAL effector proteins have been repurposed for genome engineering functions, while the extension of the ubiquitous CRISPR/Cas9 system to plants was outlined in a technical talk from Kate Caves (DNA2.0, USA), and exemplified in work described by Jen Sheen (Havard University, MA, USA) (Li et al., 2013). To inspire participants to think about the practical applications of the techniques they had learned, a talk from Ben Blount (Imperial College London, UK) and discussions led by Nicola Patron (The Sainsbury Laboratory/OpenPlant, Norwich, UK), encouraged participants to consider the advantages and disadvantages of different DNA assembly techniques for different applications (Patron, 2014), in order to select the most appropriate method for a given problem. All participants reported back that they found the talks interesting and useful, despite their varied backgrounds, and nearly all said they would apply something they had learned from the lectures to their own research, suggesting that the summer school had successfully achieved its aim of providing world-leading training to European researchers. Since the participants came from a variety of experimental backgrounds, from experienced molecular biologists to those who had never set foot in a laboratory, it was challenging to come up with a practical programme to suit the wide ability range. As a result, the practical sessions were designed to follow a logical design–build–test sequence (Fig. 1), so that they would be informative from the perspective of introducing experimental principles and exemplifying the taught content, as well as providing high-level technical details for those who were interested. Participants were assembled into multidisciplinary groups, allowing experienced experimentalists to assist those from ‘dry’ laboratory backgrounds. The practical sessions were particularly enjoyable, and it was illuminating to see the taught content put into practice. Feedback from the participants after the event suggested they found these sessions especially valuable and interesting. Despite the range of pre-existing experience, 95% reported that they found the sessions useful, with all finding them interesting. Most were confident that they would apply something they had learned to their own research. To encourage participants to consider the ethical, legal and social aspects of plant synthetic biology in the current climate, multidisciplinary teams were challenged to devise a synthetic biology-based solution to facilitate ‘sustainable intensification’ of agriculture. To encourage teamwork at the beginning, each group was given an Arduino (www.arduino.cc), an open-source, programmable electronics platform with simple hardware and software, and tasked to generate a small device with it (Fig. 1). The students were introduced to such devices as they are increasingly used as cheap technology ‘hacks’ in research, and the modular, components-based nature also provided a useful analogy for synthetic biology. Jim Haseloff then provided the context behind the projects, outlining the need for more sustainable approaches to intensive farming given the prospect of future population growth and increasing demand for finite resources. Teams were encouraged to identify a current problem with an aspect of global agriculture and design a solution, considering both the technical execution and real-world implementation. Taking inspiration from the talks given during the week, and to address some of the ethical, legal and social aspects that would need to be considered for the sustainable intensification projects, participants discussed the wider perception of plant synthetic biology technologies and whether they were currently restricted by barriers at the level of governmental regulation or public acceptance. It was noted that synthetic biology may be suffering from the negative press associated with previous research on genetically modified organisms, even though current genome editing techniques do not yield conventionally ‘transgenic’ plants. One participant observed that modification of food products, which covers a large proportion of plant synthetic biology, is a particularly emotive issue, and the perceived correlation between agritechnology and corporate capitalism risks overshadowing some of the societal benefits. It was proposed that the reluctance to accept genetically modified crops/biofuels, as opposed to pharmaceuticals, could be due to the current availability of nonmodified alternatives in these areas, which may change as the pressure of food and fuel resources intensifies. The group concluded that, as synthetic biologists, they must engage in public discussions to articulate why their work is beneficial to society, especially in the context of other available solutions. Each team pitched their idea for sustainable intensification and defended their concept in response to questions from their peers and a panel of experts from a wide range of fields, consisting of OpenPlant synthetic biologists, BBSRC policy-makers, Christian Rogers (John Innes Centre, UK) from the Engineering Nitrogen Symbiosis for Africa project, and social scientist Jason Chilvers (University of East Anglia, Norwich, UK). Proposals included introducing nitrogen-fixing capacity into crop plants; engineering drought-resistant wheat where the waste straw can be converted to bioethanol; generating a perennial rice strain with an increased nutrient content and saline tolerance; and developing a plant capable of reporting nutrient levels in the soil. The panel were impressed with the ambition of the proposals and introduced discussions about the regulation of the devised technologies and their competitiveness with existing solutions. Following the sustainable intensification task, participants agreed that their appreciation of the ethical, legal and social aspects of synthetic biology had increased, with most claiming it had made them think differently about their own research – a significant step in training responsible researchers of the future. The aim of the ERASynBio/OpenPlant summer school ‘An introduction to plant synthetic biology’ was to provide training for early career scientists to set them on the way to becoming world-class, responsible synthetic biology researchers, and in particular to impart tuition at the cutting-edge of the rapidly developing and influential field of plant synthetic biology. On this front, the summer school was a great success, and an invaluable and enjoyable opportunity for early career researchers to learn from and engage with world-leading experts in plant synthetic biology. The talks and practical sessions were especially inspiring and constructive, and feedback from the participants was overwhelmingly positive, with all saying that they would recommend future summer schools of this type to their peers. Many participants commented that the best aspect of the summer school was getting to meet and network with other researchers from around the world with diverse backgrounds and experiences. Most believed they would directly benefit from these collaborations in their future work – fulfilling the objective of working towards an integrated and connected synthetic biology community. All in all, the ERASynBio/OpenPlant summer school was an enjoyable and inspiring week that succeeded in achieving its aims for all involved, and has hopefully set a precedent for future plant synthetic biology training. The authors would like to thank OpenPlant and the John Innes Centre for hosting the summer school, Anne Osbourn and Jim Haseloff for coordination, Helen Ghirardello for organization, and James Reed (John Innes Centre), Laurence Tomlinson and Mark Youles (The Sainsbury Laboratory) for technical assistance. The authors would also like to thank ERASynBio for funding, through the European Commission Seventh Framework Programme. The John Innes Centre is supported by BBSRC Institute Strategic Programme Grants BB/J004561/1, BB/J004553/1, BB/J004588/1 and BB/J004596/1 and the John Innes Foundation, and the OpenPlant Synthetic Biology Research Centre by EPSRC/BBSRC award BB/L014130/1.