Tyler M. Earnest, John A. Cole, Joseph R. Peterson, Michael J. Hallock,
Thomas E. Kuhlman, and Zaida Luthey-Schulten.
Ribosome biogenesis in replicating cells: integration of experiment
and theory.
Biopolymers, 105:735-751, 2016.
(PMC: PMC4958520)
EARN2016-ZLS
Ribosomes—the primary macromolecular machines responsible for translating
the genetic code into proteins—are complexes of precisely folded RNA and
proteins. The ways in which their production and assembly are managed by
the living cell is of deep biological importance. Here we extend a recent
spatially resolved whole-cell model of ribosome biogenesis in a fixed volume1
to include the effects of growth, DNA replication, and cell division. All
biological processes are described in terms of reaction-diffusion master
equations and solved stochastically using the Lattice Microbes simulation
software. In order to determine the replication parameters, we construct and
analyze a series of Escherichia coli strains with fluorescently labeled genes
distributed evenly throughout their chromosomes. By measuring these cells’
lengths and number of gene copies at the single-cell level, we could fit a
statistical model of the initiation and duration of chromosome replication. We
found that for our slow-growing (120 minute doubling time) E. coli cells,
replication was initiated 42 minutes into the cell cycle and completed after an
additional 42 minutes. While simulations of the biogenesis model produce the
correct ribosome and mRNA counts over the cell cycle, the kinetic parameters
for transcription and degradation are lower than anticipated from a recent
analytical time dependent model of in vivo mRNA production. Describing
expression in terms of a simple chemical master equation, we show that the
discrepancies are due to the lack of non-ribosomal genes in the extended
biogenesis model which effects the competition of mRNA for ribosome
binding, and suggest corrections to parameters to be used in the whole-cell
model when modeling expression of the entire transcriptome.
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