Design of expression vectors for Chlamydomonas reinhardtii using domain-specific language


Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors


M. L. Wilson S. Okumoto L. Adam J. Peccoud


Published in: Bioinformatics
Volume: 30, Issue: 2, Pages: 251-257
Published: 01/15/2014
DOI: 10.1093/bioinformatics/btt646

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The design of expression vectors often requires to follow specific rules dictated by the requirements of a project. In this paper, we introduced the GenoCAD grammar editor. We demonstrated how it could be used to capture set of design rules applicable to specific biological domains. We used the development of expression vectors for expressing genes in the chloroplast of the microalgae Chlamydomonas reinhardtii as an example.

The design of expression vectors used in different biotechnology applications is based on domain-specific rules. For instance, promoters, origins of replication or homologous recombination sites are host-specific. Similarly, chromosomal integration or viral delivery of an expression cassette imposes specific structural constraints. As de novo gene synthesis and synthetic biology methods permeate many biotechnology specialties, the design of application-specific expression vectors becomes the new norm. In this context, it is desirable to formalize vector design strategies applicable in different domains.

Using the design of expression vectors targeting the chloroplast of Chlamydomonas reinhardtii as an example, we show that a vector design strategy can be formalized as a domain-specific language. We have developed a graphical editor of context-free grammars usable by biologists without prior exposure to language theory. This environment makes it possible for biologists to iteratively improve their design strategies throughout the course of a project. It is also possible to ensure that vectors designed with early iterations of the language are consistent with the latest iteration of the language.