Persisters: a distinct physiological state of E. coli

Background  

Bacterial populations contain persisters, phenotypic variants that constitute approximately 1% of cells in stationary phase and biofilm cultures. Multidrug tolerance of persisters is largely responsible for the inability of antibiotics to completely eradicate infections. Recent progress in understanding persisters is encouraging, but the main obstacle in understanding their nature was our inability to isolate these elusive cells from a wild-type population since their discovery in 1944.     

E. gracilis RNA polymerase I: a zinc metalloenzyme.

$\text{E. gracilis}$ DNA dependent RNA polymerase I has been purified to homogeneity. α-amanitin, over the concentration range 0.05 to 200 μg/ml, does not affect its activity, consistent with its being classified as an RNA polymerase I. Based on a molecular weight of 624,000 daltons the enzyme contains 2.2 g atom of Zn but no Mn, Cu, Fe, as determined by microwave excitation emission spectrometry. Zinc is essential for activity since the chelating agent, 1,10-phenanthroline, inhibits enzymatic function but its non-chelating analogue, 4,7-phenanthroline is ineffective. Thus, like the RNA polymerase II, zinc is a catalytically essential component of $\text{E. gracilis}$ RNA polymerase I (1).     

FoldEco: a model for proteostasis in E. coli

To gain insight into the interplay of processes and species that maintain a correctly folded, functional proteome, we have developed a computational model called FoldEco. FoldEco models the cellular proteostasis network of the E. coli cytoplasm, including protein synthesis, degradation, aggregation, chaperone systems, and the folding characteristics of protein clients. We focused on E. coli because much of the needed input information--including mechanisms, rate parameters, and equilibrium coefficients--is available, largely from in vitro experiments; however, FoldEco will shed light on proteostasis in other organisms. FoldEco can generate hypotheses to guide the design of new experiments. Hypothesis generation leads to system-wide questions and shows how to convert these questions to experimentally measurable quantities, such as changes in protein concentrations with chaperone or protease levels, which can then be used to improve our current understanding of proteostasis and refine the model. A web version of FoldEco is available at http://foldeco.scripps.edu.