Macromolecular complexes in the genetically minimized bacterium, JCVI-syn3A, support gene expression (RNA polymerase, ribosome, and 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 on cell membrane were considered to guarantee a high yield of assembly given the existing time scales of the gene expression. By alleviating the undesired kinetically trapped intermediates in ATP synthase assembly, the efficiency was improved, while the heterogeneity of subunit synthesis at the single-cell level greatly undermines it. The assembly of RNA polymerase, ribosome, and degradosome influence the speed and efficiency of protein synthesis. Collectively, this model predicted time-dependent cellular behaviors consistent with experiments. A deep learning analysis of the simulated time-dependent concentrations of 148 intracellular metabolites allowed the construction of a trajectory tree from which three distinct metabolic phenotypes were identified in the population of 100 cells considered. At last, we will briefly discuss extending the simulation to cover multiple cell cycles.
Fu et al. (Sun,) studied this question.