Figure 1

Cell cycle dynamics view of one wild-type in silico cell at 7 h post-cell cycle initiation. This view includes six animations which highlight the dynamics of the predicted metabolic fluxes and RNA and protein expression over the cell cycle. In particular, the view shows the onset of DNA replication, and the subsequent bidirectional movement of DNA polymerase on the chromosome. The view also highlights the onset of cytokinesis following the completion of DNA replication. (a) Instantaneous shape of M. genitalium as it initially elongates and later pinches at the septum, forming two daughter cells. (b) Metabolic map illustrating metabolite concentrations and reaction fluxes. Each metabolite is normalized to its mean concentration, and each reaction is normalized to its mean flux. Dark blue arrows indicate high reaction flux; light blue arrows indicate low reaction flux. Large circles indicate high metabolite concentrations; small circles indicate low metabolite concentrations. (c) Heatmap of the copy number of each RNA, protein monomer, and protein complex species. Each gene product is normalized to its mean copy number. Yellow indicates high expression; blue indicates low expression. (d) Instantaneous polymerization (blue), methylation (orange), strand break (red), and protein-binding status of the M. genitalium chromosomes. (e) Space-time plot illustrating the instantaneous chromosomal locations of the replication initiator DnaA and DNA polymerase. (f) Map of the protein-coding genes indicating protein synthesis. Each gene is colored according to the length of its longest nascent polypeptide. Green represents genes with one active ribosome; blue represents genes with multiple active ribosomes. An interactive version is available at http://wholecellviz.stanford.edu/cellCycle.