The question of orthogonality is inherent to the endeavor of creating standards in Synthetic Biology, although few systematic approaches have been proposed yet. In a first step, gene circuits will inevitably be designed, experimentally tested and characterized in one bacterial species, e.g. one of the model organisms as Escherichia coli. In order to use the same circuit and to maintain its original functionality in a different species/chassis, the behavior of its elements have to be assessed. For example, a circuit might require to maintain the level of expression of protein A in a certain range. When switching species, the efficiency of regulatory elements such as promoters, ribosome binding sites, and codon usage might need to be tuned in order to maintain a similar level of expression. Thus, adaptability and orthogonality of the standard biological components are key to the design and use of biological circuits.
SQrutiny is a web-based tool to assist Synthetic Biology researchers on the task of ensuring their circuits are orthogonal between widely-studied bacterial chassis models. It covers a whole design workflow, from building a new circuit piece by piece or modify existing ones, to the evaluation of a wide repertoire of regulatory signals that could be affecting the expression, such as promoters, terminators or ribosome binding sites. This tool implements a series of validated bioinformatic approaches to report the user about potential parts of the circuit that could prevent the proper expression and function of a circuit. Results can be explored either visually in the platform or by downloading them.
SQrutiny has been developed at the CRG in the frame of the BioRoboost project by the group of Design of Biological Systems. The CRG is an interdisciplinary scientific institution focused on understanding the complexity of life from the genome to the cell to a whole organism and its interaction with the environment.