Growth Rate-Dependent Global Effects on Gene Expression in Bacteria

Abstract

Summary Bacterial gene expression depends not only on specific regulations but also directly on bacterial growth, because important global parameters such as the abundance of RNA polymerases and ribosomes are all growth-rate dependent. Understanding these global effects is necessary for a quantitative understanding of gene regulation and for the robust design of synthetic genetic circuits. The observed growth-rate dependence of constitutive gene expression can be explained by a simple model using the measured growth-rate dependence of the relevant cellular parameters. More complex growth dependences for genetic circuits involving activators, repressors and feedback control were analyzed, and salient features were verified experimentally using synthetic circuits. The results suggest a novel feedback mechanism mediated by general growth-dependent effects and not requiring explicit gene regulation, if the expressed protein affects cell growth. This mechanism can lead to growth bistability and promote the acquisition of important physiological functions such as antibiotic resistance and tolerance (persistence).

Short-time movement of E. coli chromosomal loci depends on coordinate and subcellular localization

“…This suggests that local physical properties vary according to specific instants of the cell cycle, which is very plausible to expect, given the observed replication, decatenation, (de)-condensation transitions that the chromosome undergoes over a bacterial cell cycle 34,4,40 . Notably, this trend is particularly evident for the Ter macrodomain locus, which becomes less mobile at cell poles and at mid-cell, that is, probably around cell division, when the Ter macrodomain is known to be compacted by MatP and possibly externally tethered 16,18,33 .…”

“…S8). Moreover, in our experiments, the range of loci intensities can vary substantially with nutrient conditions because GFP expression (and plasmid copy number) vary with growth rate 34 . As the measured MSD includes a contribution from both physical dot displacements and dot intensity (which in turn is subject to statistical variation across tracks and loci, see Supplementary Figs S9 and S10), care is required when comparing the MSD of loci from cells grown in different nutrient conditions.…”

Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence

“…3B). A model of the hip module that uses deterministic rate equations formalism has recently been proposed to lead to bistability (30,31). We developed an alternative model in which stochasticity of chemical reactions and our experimental observations of growth-arrest duration can be explicitly implemented (Fig.…”

General calibration of microbial growth in microplate readers

“…Much of our understanding of bacterial and yeast life cycles stems from monitoring their proliferation in time and the most routine way of doing so is using optical density (OD) measurements. The applications of such measurements range from routine checks during different cloning techniques 1 ; through studying cellular physiology and metabolism 2,3 ; to determining the growth rate for antibiotic dosage 4,5 ; and monitoring of biomass accumulation during bio-industrial fermentation 6 . Here we introduce a set of calibration techniques that take into account the relevant parameters affecting OD measurements, including at high culture densities, in a range of conditions commonly used by researchers.…”