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Identification of genes influencing synthetic lethality of genetic and epigenetic alterations in translation termination factors in yeast

2011 , Kiktev, D. A. , Chernoff, Yury O. , Archipenko, A. V. , Zhouravleva, G. A.

Translation termination in eukaryotic cells is determined by proteins Sup35 (eRF3) and Sup45 (eRF1) [1], which interact with a large number of partners [2]. In yeast Saccharomyces cerevisiae, protein Sup35 can form an aggregating epigenetically inherited conformer (prion) [PSI+] [3]. This prion is carried through the cytoplasm and causes disturbances in translation termination, which are phenotypically identified as the dominant omnipotent nonsense suppression. [PSI+] variants with different properties (nonsense suppression efficiency and transmission stability in mitosis) can be obtained in the same yeast strain. The presence of prion [PSI+] leads to lethality in the haploid yeast strain carrying mutations in the gene encoding another termination factor, Sup45 [4]. We have shown that the combination in the diploid strain of some mutant alleles of the SUP45 gene in the heterozygous state with prion [PSI+] entails the death of the hybrid [5]. The synthetic lethality of prion [PSI+] and mutant allele of the sup45 gene depends both on the type of mutant allele and the prion variant. Variant [PSI+], which is a strong suppressor (“strong” [PSI+], or [PSI+]S), causes synthetic lethality with all nonsense mutations and some missense mutations sup45 in the heterozygote. Our data indicate that the lethality of hybrids is correlated with a decreased activity of the Sup45 protein in the cell in case of sup45 mutations. This paper describes a test system that allows identification of proteins that affect the stability of prion [PSI+] and/or the efficiency of translation termination by their effect on the synthetic lethality of the prion conformer Sup35 and mutant alleles of SUP45. This test system is suitable to search for proteins that affect the translation termination efficiency and/ or prion maintenance in yeast cells. Gene library screening using this test system allowed us to identify the CUR1 gene, whose influence on another prion, [URE3], was shown earlier but the effect on translation termination factors was not known.

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Brownian dynamics simulation of macromolecule diffusion in a protocell

2011 , Ando, Tadashi , Skolnick, Jeffrey

The interiors of all living cells are highly crowded with macro molecules, which differs considerably the thermodynamics and kinetics of biological reactions between in vivo and in vitro. For example, the diffusion of green fluorescent protein (GFP) in E. coli is ~10-fold slower than in dilute conditions. In this study, we performed Brownian dynamics (BD) simulations of rigid macromolecules in a crowded environment mimicking the cytosol of E. coli to study the motions of macromolecules. The simulation systems contained 35 70S ribosomes, 750 glycolytic enzymes, 75 GFPs, and 392 tRNAs in a 100 nm × 100 nm × 100 nm simulation box, where the macromolecules were represented by rigid-objects of one bead per amino acid or four beads per nucleotide models. Diffusion tensors of these molecules in dilute solutions were estimated by using a hydrodynamic theory to take into account the diffusion anisotropy of arbitrary shaped objects in the BD simulations. BD simulations of the system where each macromolecule is represented by its Stokes radius were also performed for comparison. Excluded volume effects greatly reduce the mobility of molecules in crowded environments for both molecular-shaped and equivalent sphere systems. Additionally, there were no significant differences in the reduction of diffusivity over the entire range of molecular size between two systems. However, the reduction in diffusion of GFP in these systems was still 4-5 times larger than for the in vivo experiment. We will discuss other plausible factors that might cause the large reduction in diffusion in vivo.

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