Plant Synthetic Biology


Rule-Based Design of Plant Expression Vectors Using GenoCAD


Anna Coll Mandy L. Wilson Kristina Gruden Jean Peccoud Martina Stromvik


Published in: PLOS ONE
Volume: 10, Issue: 7, Pages: e0132502-
Published: 7/6/2015
DOI: 10.1371/journal.pone.0132502

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Plant synthetic biology requires software tools to assist on the design of complex multi-genic expression plasmids. Here a vector design strategy to express genes in plants is formalized and implemented as a grammar in GenoCAD, a Computer-Aided Design software that can be used for plant synthetic biology. It includes a library of plant biological parts organized in structural categories and a set of rules describing how to assemble these parts into large constructs. Rules developed here are organized and divided into three main subsections according to the aim of the final construct: protein localization studies, promoter analysis and protein-protein interaction experiments. The GenoCAD plant grammar guides the user through the design while allowing users to customize vectors according to their needs. Therefore the plant synthetic biology grammar implemented in GenoCAD will help plant biologists take advantage of methods from synthetic biology to design expression vectors supporting their research projects.

This paper presents a vector design strategy to express genes in plants. Specifically, it includes a grammar to design constructs for three categories of experiments: promoter analysis, protein localization and protein-protein interaction (PPI) studies, which are perhaps the most demanding in plant biology. The design rules of these vectors are sufficiently different from the design of protein expression in E.coli to justify the development of a new grammar following the grammar-design workflow previously described by Wilson et al.. Constructs for promoter analysis, localization, and PPI studies are frequently used in the plant biology community. Many commercially available plasmids can be used for these applications, but they do not always meet all the requirements of specific projects. This usually forces the user to adapt the vector, and edit the sequence using a cut-and–paste approach, which has a high chance of introducing errors. Here we have captured the expertise gained by our group over the years to produce set of design rules and a parts library, which will guide non-expert users through the design process. Advanced users can use the GenoCAD grammar editor to customize this grammar by adding rules and parts to extend the scope of the grammar. Alternatively, they could also simplify the grammar by eliminating specific rules that do not apply to their projects, or even delete an entire branch of the grammar to streamline the design process.

This plant synthetic biology work is a collaboration with Anna Coll and Kristina Gruden from the National Institute of Biology in Ljubljana.