Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell

Macromolecular complexes in the genetically minimized bacterium, JCVI-syn3A, support gene expression (RNA polymerase, ribosome, degradosome), metabolism (ABC transporters, ATP synthase), and chromosome dynamics. In this work, we further incorporate the assembly of 21 unique macromolecular complexes into the existing whole-cell kinetic model of Syn3A. The synthesis and translocation of protein subunits in membrane complexes occur through distinct pathways. A range of 2D association rates for membrane complexes were considered to guarantee a high yield of assembly, given the existing time scales of gene expression. By alleviation of the undesired kinetically trapped intermediates in ATP synthase assembly, the efficiency was improved. The assembly of RNA polymerase, ribosome, and degradosome influences the speed and efficiency of protein synthesis. Collectively, this model predicted time-dependent cellular behaviors consistent with experiments. A machine learning analysis of the time-dependent metabolomics and metabolic fluxes highlighted the effect of introducing a complex assembly into our whole-cell model.