Building a cell requires an understanding of which genes (and combinations of genes) are essential for an organism to survive. Numerous efforts have identified these gene sets for different organisms, however many remain uncharacterized. We plan to distribute open source kit sets of these genes to facilitate characterization of proteins, testing of essential gene circuits, validation of essentiality, and remixing.
Hutchinson, et al (2016) minimized and synthesized the genome of Mycoplasma mycoides to create JCVI-Syn3.0. The JCVI-Syn3.0 gene set is a validated set of 473 interoperable genes essential for life, including the 149 genes annotated as having unknown function. In Stanford’s BIOE 80 Introduction to Bioengineering class, 164 undergraduates designed DNA constructs for all genes in the JCVI-Syn3.0 genome (see Building a synthetic cell with 164 undergraduates) for further details).
We are synthesizing the complete set of designed constructs for release under the OpenMTA in a standardized and open distribution vector, codon optimized for E. coli. The gene library will be available through the BioNet and other means.
We hope that this first library will allow interested biologists worldwide to probe the functions of the unknown genes, “perhaps earning several Nobel Prizes along the way” (Alberts 2016).
We intend to follow the JCVI-Syn3.0 gene set with an identical kit containing the union of known-essential Mesoplasma florum genes, and genes identified as homologous to the JCVI-Syn3.0 essential set. This kit will allow for easy experimentation with genes from an easier to handle (non-pathogenic) organism.
As a component of the BIOE 80 course, students also identified E. coli genes coding for the essential functions represented by the JCVI-Syn3.0 gene set (see the poster). We will distribute a kit of these genes, as well as all E. coli genes identified as essential in the Keio collection (Baba 2006).
In combination with in-vitro and in-vivo testing systems, we believe that these gene kits will support the rapid development of genetic modules for essential organism function, and rapid integration of these modules into higher-level systems.