A modular minimal cell model: purine and pyrimidine transport and metabolism

Abstract

A more complete understanding of the relationship of cell physiology to genomic structure is desirable. Because of the intrinsic complexity of biological organisms, only the simplest cells will allow complete definition of all components and their interactions. The theoretical and experimental construction of a minimal cell has been suggested as a tool to develop such an understanding. Our ultimate goal is to convert a "coarse-grain" lumped parameter computer model of Escherichia coli into a genetically and chemically detailed model of a "minimal cell." The base E. coli model has been converted into a generalized model of a heterotrophic bacterium. This coarse-grain minimal cell model is functionally complete, with growth rate, composition, division, and changes in cell morphology as natural outputs from dynamic simulations where only the initial composition of the cell and of the medium are specified. A coarse-grain model uses pseudochemical species (or modules) that are aggregates of distinct chemical species that share similar chemistry and metabolic dynamics. This model provides a framework in which these modules can be "delumped" into chemical and genetic descriptions while maintaining connectivity to all other functional elements. Here we demonstrate that a detailed description of nucleotide precursors transport and metabolism is successfully integrated into the whole-cell model. This nucleotide submodel requires fewer (12) genes than other theoretical predictions in minimal cells. The demonstration of modularity suggests the possibility of developing modules in parallel and recombining them into a fully functional chemically and genetically detailed model of a prokaryote cell.

Figures

Fig. 1.

A sketch of the mixed minimal cell model, including diagrammatic inclusion of a genetically detailed nucleotide pathway (enclosed arrow in box), growing in a glucose, ammonium, free bases medium with glucose as the limiting nutrient. Solid lines and dashed lines indicate the flow of material and information, respectively. A1, ammonium ion; A2, glucose; P1, amino acids; PG, ppGpp; P2, free bases; P3, deoxyribonucleotides; P4, cell envelope precursors; M1, protein; M2RTI, immature “stable” RNA; M2RTM, mature r-RNA and t-RNA; M3, DNA; M2M, messenger RNA; W, waste products (CO2, H2O, and acetate); M4, nonprotein part of cell envelope; M5, glycogen; E1, enzyme that converts P2 to P3; E2, E3, molecules involved in crosswall formation and cell envelope synthesis. *, the material is present in the external environment (adapted from ref. 26).

Fig. 2.

Pyrimidine nucleotide salvage and biosynthesis pathway.

Fig. 3.

Purine nucleotide salvage and biosynthesis pathway.

Fig. 4.

Relative cell volume (absolute cell volume/maximum cell volume) as a function of relative growth rate (absolute growth rate/maximum growth rate) for E. coli. Open circles, closed squares, open triangles, closed triangles, continuous line, and dashed line represent measurements from the Coulter Counter [(26); refs. and 78]; volumes calculated from electron microscopy measurements of cell dimension with gluteraldehyde-fixed cells, the Cornell E. coli model; mixed minimal cell model, respectively.

Fig. 5.

Relative RNA composition (absolute % RNA/maximum % RNA) of a variety of bacteria at different relative growth rates. Open squares, open triangles, full circles, asterisks, full diamonds, and continuous line represent E. coli (73); K. aerogenes (74); A. calcoaceticus (75); A. aerogenes (76); Bacillus megaterium (76), and mixed minimal cell model, respectively.