Jason T. Noel | Searcharxiv

arXiv2008

Gene regulation in continuous cultures: A unified theory for bacteria and yeasts

During batch growth on mixtures of two growth-limiting substrates, microbes consume the substrates either sequentially or simultaneously. These growth patterns are manifested in all types of bacteria and yeasts. The ubiquity of these growth patterns suggests that they are driven by a universal mechanism common to all microbial species. In previous work, we showed that a minimal model accounting only for enzyme induction and dilution explains the phenotypes observed in batch cultures of various wild-type and mutant/recombinant cells. Here, we examine the extension of the minimal model to continuous cultures. We show that: (1) Several enzymatic trends, usually attributed to specific regulatory mechanisms such as catabolite repression, are completely accounted for by dilution. (2) The bifurcation diagram of the minimal model for continuous cultures, which classifies the substrate consumption pattern at any given dilution rate and feed concentrations, provides a a precise explanation for the empirically observed correlation between the growth patterns in batch and continuous cultures. (3) Numerical simulations of the model are in excellent agreement with the data. The model captures the variation of the steady state substrate concentrations, cell densities, and enzyme levels during the single- and mixed-substrate growth of bacteria and yeasts at various dilution rates and feed concentrations. (4) This variation is well-approximated by simple analytical expressions that furnish physical insights into the steady states of continuous cultures. The minimal model provides a framework for quantitating the effect of regulatory mechanisms. We illustrate this by analyzing several data sets from the literature.

q-bio.CB↗

arXiv2005

Identification of the growth-limiting step in continuous cultures from initial rates measured in response to substrate-excess conditions

When steady state chemostat cultures are abruptly exposed to substrate-excess conditions, they exhibit long lags before adjusting to the new environment. The identity of the rate-limiting step for this slow response can be inferred from the initial yields and specific growth rates measured by exposing steady state cultures at various dilution rates to substrate-excess conditions. We measured these parameters for glucose-limited cultures of E. coli ML308 growing at various dilution rates between 0.03 and 0.6 1/hr. In all the cases, the initial yields were 20-30% less than the steady state yields. The decline of the yield implies that overflow metabolism is triggered in response to excess glucose. It is therefore unlikely that the initial response of the cells is limited by substrate uptake. The initial specific growth rates of cultures growing at low dilution rates (D = 0.03, 0.05, 0.075, 0.1, 0.3 1/hr) were significantly higher than the steady state specific growth rates. However, the increment in the specific growth rate decreased with the dilution rate, and at D=0.6 1/hr, there was no improvement in the specific growth rate. The initial specific growth rates varied hyperbolically with the dilution, decreasing sharply at dilution rates below 0.1 1/hr and saturating at D=0.6 1/hr. This is consistent with a picture in which the initial response is limited by the activity of glutamate dehydrogenase.

q-bio.MN↗