Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli.

BACKGROUND: Proper phosphate signaling is essential for robust growth of Escherichia coli and many other bacteria. The phosphate signal is mediated by a classic two component signal system composed of PhoR and PhoB. The PhoR histidine kinase is responsible for phosphorylating/dephosphorylating the response regulator, PhoB, which controls the expression of genes that aid growth in low phosphate conditions. The mechanism by which PhoR receives a signal of environmental phosphate levels has remained elusive. A transporter complex composed of the PstS, PstC, PstA, and PstB proteins as well as a negative regulator, PhoU, have been implicated in signaling environmental phosphate to PhoR. RESULTS: This work confirms that PhoU and the PstSCAB complex are necessary for proper signaling of high environmental phosphate. Also, we identify residues important in PhoU/PhoR interaction with genetic analysis. Using protein modeling and docking methods, we show an interaction model that points to a potential mechanism for PhoU mediated signaling to PhoR to modify its activity. This model is tested with direct coupling analysis. CONCLUSIONS: These bioinformatics tools, in combination with genetic and biochemical analysis, help to identify and test a model for phosphate signaling and may be applicable to several other systems.

Contribution of Signaling Partner Association to Strigolactone Receptor Selectivity.

The parasitic plant witchweed, Striga hermonthica, results in agricultural losses of billions of dollars per year. It perceives its host via plant hormones called strigolactones, which act as germination stimulants for witchweed. Strigolactone signaling involves substrate binding to the strigolactone receptor, followed by substrate hydrolysis and a conformational change from an inactive, or open state, to an active, or closed state. In the active state, the receptor associates with a signaling partner, MAX2. Recently, it was shown that this MAX2 association process acts as a strong contributor to the uniquely high signaling activity observed in ShHTL7; however, it is unknown why ShHTL7 has enhanced MAX2 association affinity. Using an umbrella sampling molecular dynamics approach, we characterized the association processes of AtD14, ShHTL7, a mutant of ShHTL7, and ShHTL6 with MAX2 homologue OsD3. From these results, we show that ShHTL7 has an enhanced standard binding free energy of OsD3 compared to those of the other receptors. Additionally, our results suggest that the overall topology of the T2/T3 helix region is likely an important modulator of MAX2 binding. Thus, differences in MAX2 association, modulated by differences in the T2/T3 helix region, are a contributor to differences in signaling activity between different strigolactone receptors.

Polarizable Molecular Dynamics Simulations of Two c-kit Oncogene Promoter G-Quadruplexes: Effect of Primary and Secondary Structure on Loop and Ion Sampling.

G-quadruplexes (GQs) are highly ordered nucleic acid structures that play fundamental roles in regulating gene expression and maintaining genomic stability. GQs are topologically diverse and enriched in promoter sequences of growth regulatory genes and proto-oncogenes, suggesting that they may serve as attractive targets for drug design at the level of transcription rather than inhibiting the activity of the protein products of these genes. The c-kit promoter contains three adjacent GQ-forming sequences that have proposed antagonistic effects on gene expression and thus are promising drug targets for diseases such as gastrointestinal stromal tumors, mast cell disease, and leukemia. Because GQ stability is influenced by primary structure, secondary structure, and ion interactions, a greater understanding of GQ structure, dynamics, and ion binding properties is needed to develop novel, GQ-targeting therapeutics. Here, we performed molecular dynamics simulations to systematically study the c-kit2 and c-kit* GQs, evaluating nonpolarizable and polarizable force fields (FFs) and examining the effects of base substitutions and cation type (K+, Na+, and Li+) on the dynamics of their isolated and linked structures. We found that the Drude polarizable FF outperformed the additive CHARMM36 FF in two- and three-tetrad GQs and solutions of KCl, NaCl, and LiCl. Drude simulations with different cations agreed with the known GQ stabilization preference (K+ > Na+ > Li+) and illustrated that tetrad core-ion coordination differs as a function of cation type. Finally, we showed that differences in primary and secondary structure influence loop sampling, ion binding, and core-ion energetics of GQs.