Rule-Based Design of Plant Expression Vectors Using GenoCAD

<div><p>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 for 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 grammar implemented in GenoCAD will help plant biologists take advantage of methods from synthetic biology to design expression vectors supporting their research projects.</p></div

Example of three different designs for localization studies purposes as developed with the plant grammar.

<p>A. Scheme of the most basic structure we can design, where the expression cassette includes the GEN fused to a FTG by means of a LNK domain on the N terminal. B. Sample design includes an expression cassette with 2 PRO and a GEN fused to a FTG on the N terminal and to an ETG on the C terminal. C. Same as B but with the expression cassette in reverse orientation.</p

Example of two different designs for promoter analysis studies.

<p>A. The expression cassette includes a FTG under the control of a NPRO and fused with an ETG by means of a LNK. B. The expression cassette has reverse orientation and double TER.</p

Example of three different designs obtained following <i>ppi</i> route.

<p>A) <i>bifc</i> route. B) <i>coip</i> route using MYC and HA as epitope tags. C) <i>coip</i> route using GFP and HIS as epitope tags.</p

SBOL: A community standard for communicating designs in synthetic biology

<p>Abstract</p> <p>The Synthetic Biology Open Language (SBOL) is a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-adopted, formalized format for exchange between software tools, research groups, and commercial service providers. The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. As a community-driven standard, SBOL adapts as synthetic biology evolves, providing specific capabilities for different aspects of the synthetic biology workflow. The SBOL Developers Group has implemented SBOL 1.1 as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. This paper also reports on early successes, including a demonstration of the utility of SBOL for information exchange between three different tools from three academic sites.</p> <p> </p