No abstract

Transcriptional regulation is a key mechanism that controls the fate and response of cells to diverse signals. Therefore, the identification of the DNA-binding proteins, which mediate these signals, is a crucial step in elucidating how cell fate is regulated. In this report, we applied both bioinformatics and functional genomic approaches to scrutinize the unusually large promoter of the IME1 gene in budding yeast. Using a recently described fluorescent protein-based reporter screen, reporter-synthetic genetic array (R-SGA), we assessed the effect of viable deletion mutants on transcription of various IME1 promoter-reporter genes. We discovered potential transcription factors, many of which have no perfect consensus site within the IME1 promoter. Moreover, most of the cis-regulatory sequences with perfect homology to known transcription factor (TF) consensus were found to be nonfunctional in the R-SGA analysis. In addition, our results suggest that lack of conservation may not discriminate against a TF regulatory role at a specific promoter. We demonstrate that Sum1 and Sok2, which regulate IME1, bind to nonperfect consensuses within nonconserved regions in the sensu stricto Saccharomyces strains. Our analysis supports the view that although comparative analysis can provide a useful guide, functional assays are required for accurate identification of TF-binding site interactions in complex promoters.

An experimental study of CHT photolysis at 2537 Å in argon and nitrogen (N2) matrices is presented. The sole IR detectable product is identified as BCHD:  bicyclo[3.2.0]hepta-2,6-diene. It is found that CHT molecules trapped in spectroscopically distinct sites were converted to the product at different rates. In the initial stages of the photolysis, the population of some CHT trapping sites increased, indicating site population transfer. In the long run, however, all sites were depleted. Molecular dynamics simulations are performed to estimate the structure of the different sites, and together with a kinetic model, are used to account for the UV induced changes. A tentative energy level diagram of the system is offered, in an attempt to rationalize the total absence of toluene which is formed predominantly in the gas-phase irradiation of CHT at this wavelength. The “twin state” concept is instrumental in this rationalization.

Molecular dynamics simulations of the trapping of molecules in a rare gas matrix are presented. In distinction with most previous simulations, a site's structure is not obtained by a guess and optimize method, but is found by allowing the lattice to grow by adding atoms from the vapor onto a “seed” crystal. Simple pairwise potentials are used to simulate the growth of rare gas matrices containing some small guests, including diatomic and triatomic molecules. Changes in the structure and energy of the solid are calculated, as well as the vibrational frequencies of the trapped molecules, providing an estimate for the matrix shift. The method also allows the estimate of small changes in the interatomic distances in the trapped molecules, as compared to the gas phase values. Novel site geometries, in which the host lattice atoms are displaced from their equilibrium crystal positions, are observed for guest molecules that can strongly distort the lattice because of asymmetry or size mismatches.