ChassiDex

While iGEM teams and the synthetic biology community has mostly focussed on developing DNA parts called ‘BioBricks’ for use in biological systems, the parts have to be ultimately used in an organism called host or sometimes even ‘chassis’. For most projects, researchers try to stick with using a few familiar model organisms such as Escherichia coli for the host system requirements. Lack of experience is often a reason to avoid unfamiliar yet apt organisms for the project at hand. To explain this with an analogy, imagine Taxi-hailing apps being available only for desktop computers because the developers do not know how to develop applications that run on mobile phones. Hence, in the 2017 edition of iGEM, Team IIT Madras worked on developing a database of host organisms called ChassiDex that aimed to curate different organisms along with all the information about them that is relevant in the context of synthetic biology. The idea of having such a database was very well received by the synthetic biology community that attended the iGEM Giant Jamboree in 2017. We have continued working on the project and revamping it with suggestions received, with the hope to improve this project and create a team to manage the database. The website for the database is available at Chassidex.org.
Additionally, We also developed some independent tools to help make life easier for synthetic biologists. These include CUTE,a codon table generator and ComicSyns,a font for synthetic biologists.

We looked up the literature for Acinetobacter baylyi ADP1 but could not find substantial literature backing. The literature was too less and not many tools were available to do synthetic biology experiments with this organism. So, This was the motivation to generate a toolbox for Acinetobacter baylyi and try to make it as generic as possible so that if any other team or research groups wish to work with other organism then they can used these tools.

The first thing that is required for any synthetic biology experiments are fluorescent reporter proteins. We wished to codon optimize GFP and mCherry for A. baylyi. However, when we asked the companies to codon optimize the fluoroscent proteins, the problem with companies was they did not have the codon bias table for A. baylyi.

Solution 1: We made a free use online tool called CUTE (codon usage table enumerator) that can generate Codon usage table by taking into consideration the protein coding annotation. This tool can be used for any other organism whose Genome has been sequences and protein coding regions are annotated. Cute can be found on the CUTE ChassiDex.
We generated the codon usage table as the protein annotation of A. baylyi is available on the NCBIwebsite. Using this codon table, we codon optimized reporter proteins and its characterization can be found here.

Solution 2: Next we move on to building a Synthetic promoter library for Acinetobacter baylyi ADP1 but we wanted to make the promoter library as generic as possible. So we made a T5 promoter based library which can have varying strengths. This library can be extremely useful for metabolic engineering and synthetic biology experiments.