Essential Metabolism for a Minimal Cell

The question of the core requirements of cellular life led to the construction of the "minimal cell" JCVI-syn3A: A cell where practically all genes were removed that were not essential for robust growth in a stress-free laboratory environment. With only 493 genes in a 543 kbp genome, JCVI-syn3A has a genome smaller than that of any independently-replicating cell found in nature. It provides a versatile platform to study the basics of cellular life and is small enough that a complete description of all cellular functions can be pursued.

Here, we present an extensively curated metabolic reconstruction and flux balance analysis (FBA) model of this minimal cell, using the vast amount of experimental information available on its natural precursor, Mycoplasma mycoides capri. The model, featuring 337 reactions involving 304 metabolites, is near-complete with 98 % of enzymatic reactions justified through gene assignments and/or experimental evidence, and agrees well with gene essentiality data from transposon mutagenesis experiments. The 155 genes included in the reconstruction have a high in vivo essentiality or quasi-essentiality of 92 %, compared to 79 % in silico essentiality–underscoring the minimality of the network. The reconstruction itself and the comparison of in vivo and in silico essentialities lead to new hypotheses on particular metabolic functions, suggesting specific experiments. Thus, the model provides a solid foundation for further experimental and computational studies on the minimal cell.