Free tools for plant trait development

The OpenPlant initiative supports two tiers of research activities.

Development of open tools that will underpin systematic approaches to bioengineering of plants:

  1. A common syntax for plant DNA parts and hierarchical assembly of genetic circuits.
  2. Open DNA registries for sharing information, to join an international web of registries with plant specific DNA parts. 
  3. Legal tools for open exchange of DNA parts and other reagents in biotechnology.
  4. Establishment of a database and archive for publication of DNA part descriptions.
  5. Development of a major new lower plant system as a simple and facile chassis for Synthetic Biology, to enable high throughput screening and analysis at the cellular scale.
  6. New DNA parts for the control and quantitative imaging of genetic circuits in plants.
  7. Techniques for routine genome-scale engineering in plants. 
  8. Software tools with improved performance for DNA part catalogues, automated assembly, modelling of synthetic gene circuits and cellular morphogenesis.

Application of these approaches to the engineering of new traits in plants: 

  1. Altered photosynthesis and leaf structure.
  2. Changes in plant carbohydrate content.
  3. Engineered pathways for the metabolic engineering of natural products.
  4. New forms of symbiosis and nitrogen fixation for crop plants.
  5. Methods for high level production of biomolecules by transient expression.

Download PDF copy of the OpenPlant Handbook 2017 - revised 19 Sept 2017

 

Annual Progress Reports

Year 2: Download PDF version of Annual Report 2015-2016 (851 KB)

Executive Summary: In our second year of operation (Sept 2015-2016), we made notable progress in development of: (i) foundational technologies for standardised DNA assembly in plants, and simple systems for plant synthetic biology, (ii) trait development with improved capacity for metabolic analysis and reprogramming of metabolism in plants, and (iii) activities for outreach and responsible innovation.

Foundational work

  • Commissioned advanced imaging/robotics equipment at the Cambridge OpenPlant lab.
  • Completion of genome sequence and transcript map of the Cam-1 (male) and Cam-2 (female) isolates of Marchantia polymorpha. Data will be included in forthcoming publication of genome.
  • High resolution map of the time course of gene expression during sporeling germination and chloroplast differentiation.
  • Construction of MarpoDB, a genecentric database for mining and describing DNA parts from Marchantia (http://marpodb.io)
  • Official acceptance of the common syntax for plant DNA parts as a new standard (Phytobricks) in the iGEM 2016 competition, and introduction of an award for plant work.
  • Development of Phytobrick and UNS standards for efficient hierarchical assembly of DNA circuits.
  • Expansion of a Chlamydomonas DNA toolkit for target gene expression and assay of miRNA-dependent gene silencing.
  • Development of a suite of Cas9 variants and toolkit for targeted mutagenesis and gene deletion in multiple plant species.
  • Construction of series of vectors for fine tuning of protein expression using HyperTrans system
  • Methods for mining plant genomes for biosynthetic gene clusters

Trait Development

  • Design and synthesis of an artificial protein scaffold library, built to the Phytobrick standard and verified by BiFC.
  • Production of cell-specific epitope tags for identifying DNA motifs that drive gene expression in photosynthetic tissues in Arabidopsis.
  • Publication of a novel reporter for chloroplast transformation, and identification of transit peptides for chloroplast localisation of nuclear encoded products in Marchantia.
  • Identification of a large repertoire of carbohydrate active enzymes in Euglena gracilis.
  • Transformation of gene editing constructs into potato, to create digestion-resistant starches, and preliminary screening of transformed plantlets.
  • Gram-scale production of triterpenes for analysis and assay, using the HyperTrans system.
  • Production of the plant-derived iridoid alkaloid strictosidine in yeast.
  • Generation of a trichome-specific protein database for enzyme discovery.
  • Asteraceae P450 proteins as a toolkit for targeted modification of sesquiterpenes.
  • Development of the HyperTrans system for use in tomato.
  • Screening tomato introgression lines for regulators of monoterpene biosynthesis.
  • Yeast one-hybrid analysis for the identification of transcription factors that regulate triterpene metabolic gene clusters.
  • Characterisation of gene targets for AtMYB12 and SIMYB12 in tomato, for enhancing phenylpropanoid metabolism and high levels of resveratrol and genistin production.
  • Construction of a synthetic gene cluster for dhurrin biosynthesis in Arabidopsis roots. 
  • Construction and distribution of HyperTrans DNA vectors that are compatible with the Phytobrick standard.
  • Testing of the HyperTrans system in Marchantia and BY2 cells.
  • Consultation on the design of the Norwich Research Park LeafSystems high throughput production facility, due for completion in Q2 2017.

Outreach and Responsible Innovation

  • Funded of 30 mini-grants that incorporate broad interdisciplinarity and collaboration between Cambridge and Norwich, including projects for SynBio training and capacity building in Africa and resources for schools and universities in South America.
  • Cambridge-JIC iGEM2015 team won a gold medal at the international Jamboree, with a hardware project entitled “OpenScope”.
  • Support for a joint Cambridge-JIC iGEM2016 undergraduate team with a plant-based project: chloroplast engineering in Chlamydomonas. Obtained co-sponsorship from Cambridge Consultants and Wellcome Trust/BBSRC/SEB fund.
  • Developing collaborative projects through the Virtual Institute of Responsible Innovation. 
  • OpenPlant researchers contribute to a Bioengineering Horizon Scanning Exercise run by CSER. Workshop in November 2016. Outcomes will be published in a co-authored paper.
  • Responsible and Open Innovation workshop with Dr. Kathy Liddell, Law Faculty, Cambridge.
  • OpenPlant continues to work with international IP working group and collaborate with the Biobricks Foundation to implement OpenMTA and facilitate exchange of DNA parts.
  • OpenPlant participated in the inaugural meeting of BioNet group at Asilomar and supports an open technology platform for exchange and tracking of biomaterials (http://www.bionet.io).
  • OpenPlant is supporting a workshop on ‘Genetic Resources in the Age of the Nagoya Protocol and gene/genome synthesis’ in November 2016 (led by Dominic Berry, Edinburgh).
  • Organised OpenPlant All Hands meeting for scientific exchange, Newmarket.
  • Participated in Open Technology for Biology workshop, Chile.
  • OpenTechnology Week events in Cambridge, including Technology for the Bottom Billion workshop and Makethon, coordinated with the Centre for Global Equality.
  • Workshops on ethics and openness, outreach for OpenPlant scientists with the SAW Trust, and BBSRC Media Training (March 2016). Also ran joint training workshops and provided support for synthetic biology outreach activities at Edinburgh SBRC.
  • Showcased OpenPlant science in interactive exhibits and workshops at festivals and schools workshops, including Latitude Festival (Suffolk; July 2016).
  • Nineteen graduate students are participating in projects funded by the OpenPlant Fund. Three PhD students have been recruited directly to OpenPlant (Cambridge) this year. 
  • Undergraduates have formed a student society for Synthetic Biology at the University of Cambridge (http://cusbs.soc.srcf.net) with OpenPlant support.
  • Students and postdocs at OpenPlant institutes are being recruited to share projects, resources and equipment, through ROC, a group of self organised, highly effective junior researchers.

 

Year 1:   Download PDF version of Annual Report 2014-2015 (253 KB)

Executive Summary

The Open Plant initiative aims to (i) accelerate the development of new tools and methods for plant synthetic biology, (ii) provide mechanisms for open exchange of resources, (iii) apply these standardised tools to world-leading projects in trait development, and (iv) facilitate interdisciplinary exchange, discussion and outreach.

Major achievements over the the first year of the project have been:

  • Refurbishment and equipping of new OpenPlant laboratories in Cambridge and Norwich.
  • Establishment of a common genetic syntax for exchange of DNA parts for plants, extensible to all eukaryotes (Patron et al., 2015; RFC106).
  • Drafting of an Open Materials Transfer Agreement, a simple, standardized legal tool to enable sharing of materials and associated data on a more open basis.
  • Implementation of a “single-click” OSX-installable version of the JBEIR-ICE open source DNA registry and DNA manipulation software.
  • Development of routine methods for transformation and gene editing in Marchantia polymorpha.
  • Development of Marchantia paleacea as a new system for engineering actinomycorrhizal associations.
  • Generation of draft genome and transcriptome maps for M. polymorpha and M. paleacea.
  • Characterisation of miR1157 and miR1162 precursors for use as synthetic gene regulators in Chlamydomonas reinhardtii.
  • Refactoring and use of the HyperTrans system for rapid testing of DNA circuits for terpene synthesis in Nicotiana benthamiana.
  • Funding of 16 mini-grants that incorporate broad interdisciplinarity and collaboration between Cambridge and Norwich - including hardware, wetware development and support for collaboration between OpenPlant and African scientists.
  • Support for a joint Cambridge-JIC iGEM2015 team in the Hardware Track.
  • Support for a Synbio Beta Activate event in Cambridge, to promote entrepreneurial interactions.
  • Organisation of the OpenPlant Forum and international exchange.
  • Delivery of two summer schools on Plant Synthetic Biology and CRISPR Technology in Plants, co-sponsored by ERA-SynBio and Plant Methods/GarNET, respectively.        
  • Delivery of three Science, Art and Writing educational workshops, and two school outreach events.