Exploring the mono-/bistability range of positively autoregulated signaling systems in the presence of competing transcription factor binding sites

Binding of transcription factor (TF) proteins to regulatory DNA sites is key to accurate control of gene expression in response to environmental stimuli. Theoretical modeling of transcription regulation is often focused on a limited set of genes of interest, while binding of the TF to other genomic sites is seldom considered. The total number of TF binding sites (TFBSs) affects the availability of TF protein molecules and sequestration of a TF by TFBSs can promote bistability. For many signaling systems where a graded response is desirable for continuous control over the input range, biochemical parameters of the regulatory proteins need be tuned to avoid bistability. Here we analyze the mono-/bistable parameter range for positively autoregulated two-component systems (TCSs) in the presence of different numbers of competing TFBSs. TCS signaling, one of the major bacterial signaling strategies, couples signal perception with output responses via protein phosphorylation. For bistability, competition for TF proteins by TFBSs lowers the requirement for high fold change of the autoregulated transcription but demands high phosphorylation activities of TCS proteins. We show that bistability can be avoided with a low phosphorylation capacity of TCSs, a high TF affinity for the autoregulated promoter or a low fold change in signaling protein levels upon induction. These may represent general design rules for TCSs to ensure uniform graded responses. Examining the mono-/bistability parameter range allows qualitative prediction of steady-state responses, which are experimentally validated in the E. coli CusRS system.

A balancing act in transcription regulation by response regulators: titration of transcription factor activity by decoy DNA binding sites

Studies of transcription regulation are often focused on binding of transcription factors (TFs) to a small number of promoters of interest. It is often assumed that TFs are in great excess to their binding sites (TFBSs) and competition for TFs between DNA sites is seldom considered. With increasing evidence that TFBSs are exceedingly abundant for many TFs and significant variations in TF and TFBS numbers occur during growth, the interplay between a TF and all TFBSs should not be ignored. Here, we use additional decoy DNA sites to quantitatively analyze how the relative abundance of a TF to its TFBSs impacts the steady-state level and onset time of gene expression for the auto-activated Escherichia coli PhoB response regulator. We show that increasing numbers of decoy sites progressively delayed transcription activation and lowered promoter activities. Perturbation of transcription regulation by additional TFBSs did not require extreme numbers of decoys, suggesting that PhoB is approximately at capacity for its DNA sites. Addition of decoys also converted a graded response to a bi-modal response. We developed a binding competition model that captures the major features of experimental observations, providing a quantitative framework to assess how variations in TFs and TFBSs influence transcriptional responses.

Gas-Liquid Chromatographic Method for the Analysis of Microencapsulated Ethyl Parathion and Methyl Parathion Insecticides: Collaborative Study

The determination of ethyl parathion in Penncap-E insecticide was studied collaboratively by 14 laboratories. The assay of methyl parathion in Penncap-M insecticide was studied by 8 laboratories. The original method which was adopted official first action for methyl parathion specified dimethoate, which is currently classified as a suspected carcinogen, as the internal standard. The current collaborative efforts were conducted as a supplemental study to evaluate the performance of the new internal standard, bis-2-methoxyethyl phthalate, and to test the gas-liquid chromatographic method for microencapsulated ethyl parathion (internal standard, dibutyl phthalate). The method uses essentially the same grinding and extraction with acetonitrile as the original study. At the 20% methyl parathion level, the standard deviation within laboratories was 0.186%, and among laboratories, 0.737%. Two formulations of ethyl parathion at approximately 16 and 24% were analyzed in replicate on 2 days by the same analyst, and provided excellent agreement within laboratories as well as among laboratories. The standard deviation (pooled) within laboratories was 0.284% and among laboratories, 0.518%. The method has been adopted as official first action.