49 research outputs found
A Coarse-Grained Biophysical Model of E. coli and Its Application to Perturbation of the rRNA Operon Copy Number
We propose a biophysical model of Escherichia coli that predicts growth rate
and an effective cellular composition from an effective, coarse-grained
representation of its genome. We assume that E. coli is in a state of balanced
exponential steadystate growth, growing in a temporally and spatially constant
environment, rich in resources. We apply this model to a series of past
measurements, where the growth rate and rRNA-to-protein ratio have been
measured for seven E. coli strains with an rRNA operon copy number ranging from
one to seven (the wild-type copy number). These experiments show that growth
rate markedly decreases for strains with fewer than six copies. Using the
model, we were able to reproduce these measurements. We show that the model
that best fits these data suggests that the volume fraction of macromolecules
inside E. coli is not fixed when the rRNA operon copy number is varied.
Moreover, the model predicts that increasing the copy number beyond seven
results in a cytoplasm densely packed with ribosomes and proteins. Assuming
that under such overcrowded conditions prolonged diffusion times tend to weaken
binding affinities, the model predicts that growth rate will not increase
substantially beyond the wild-type growth rate, as indicated by other
experiments. Our model therefore suggests that changing the rRNA operon copy
number of wild-type E. coli cells growing in a constant rich environment does
not substantially increase their growth rate. Other observations regarding
strains with an altered rRNA operon copy number, such as nucleoid compaction
and the rRNA operon feedback response, appear to be qualitatively consistent
with this model. In addition, we discuss possible design principles suggested
by the model and propose further experiments to test its validity
Ubiquinone accumulation improves osmotic-stress tolerance in Escherichia coli
Bacteria are thought to cope with fluctuating environmental solute concentrations primarily by adjusting the osmolality of their cytoplasm. To obtain insights into underlying metabolic adaptions, we analyzed the global metabolic response of Escherichia coli to sustained hyperosmotic stress using non-targeted mass spectrometry. We observed that 52% of 1,071 detected metabolites, including known osmoprotectants, changed abundance with increasing salt challenge. Unexpectedly, unsupervised data analysis revealed a substantial increase of most intermediates in the ubiquinone-8 (Q8) biosynthesis pathway and a 110-fold accumulation of Q8 itself, as confirmed by quantitative lipidomics. We then demonstrate that Q8 is necessary for acute and sustained osmotic stress tolerance using Q8 mutants and tolerance rescue through feeding non-respiratory Q8 analogues. Finally, in vitro
experiments with artificial liposomes reveal mechanical membrane stabilization as a principal mechanism of Q8-mediated osmoprotection. Thus, we find that besides regulating intracellular osmolality, E. coli enhances its cytoplasmic membrane stability to withstand osmotic stress