The tRNA-induced conformational activation of human mitochondrial phenylalanyl-tRNA synthetase

All class II aminoacyl-tRNA synthetases (aaRSs) are known to be active as functional homodimers, homotetramers, or heterotetramers. However, multimeric organization is not a prerequisite for phenylalanylation activity, as monomeric mitochondrial phenylalanyl-tRNA synthetase (PheRS) is also active. We herein report the structure, at 2.2 A resolution, of a human monomeric mitPheRS complexed with Phe-AMP. The smallest known aaRS, which is, in fact, 1/5 of a cytoplasmic analog, is a chimera of the catalytic module of the alpha and anticodon binding domain (ABD) of the bacterial beta subunit of (alphabeta)2 PheRS. We demonstrate that the ABD located at the C terminus of mitPheRS overlaps with the acceptor stem of phenylalanine transfer RNA (tRNAPhe) if the substrate is positioned in a manner similar to that seen in the binary Thermus thermophilus complex. Thus, formation of the PheRS-tRNAPhe complex in human mitochondria must be accompanied by considerable rearrangement (hinge-type rotation through approximately 160 degrees) of the ABD upon tRNA binding.     

PAK1 regulates myosin II-B phosphorylation, filament assembly, localization and cell chemotaxis

Serine/threonine p21-activated kinase is an effector of Rac with a key role in the regulation of cytoskeletal organization. Non-muscle myosin II is a molecular motor, which is an important component of the cytoskeleton. Non-muscle myosin II-B plays a major role in cell motility and chemotaxis. We investigated the role of Rac and p21-activated kinase 1 (PAK1) in the regulation of myosin II-B in prostate cancer cells in response to epidermal growth factor (EGF) stimulation. We found that both Rac and PAK1 affect EGF-dependent non-muscle heavy chain II-B localization and cell morphology. We further found that a dominant negative mutant of PAK1 significantly inhibits EGF-dependent myosin II-B heavy chains phosphorylation and filament disassembly. Furthermore, cells expressing the dominant negative mutant exhibited an increase in EGF-dependent myosin light chain phosphorylation and diminished chemotaxis towards EGF. To our knowledge this is the first report exploring the role of PAK1 in the regulation of both non-muscle myosin II-B heavy chains and light chains. Furthermore, the data presented here suggest that PAK1 plays a crucial role in the regulation of cell morphology and chemotaxis by regulating the phosphorylation and cellular localization of myosin II-B.     

Adaptive search space pruning in complex strategic problems

People have limited computational resources, yet they make complex strategic decisions over enormous spaces of possibilities. How do people efficiently search spaces with combinatorially branching paths? Here, we study players’ search strategies for a winning move in a “k-in-a-row” game. We find that players use scoring strategies to prune the search space and augment this pruning by a “shutter” heuristic that focuses the search on the paths emanating from their previous move. This strong pruning has its costs—both computational simulations and behavioral data indicate that the shutter size is correlated with players’ blindness to their opponent’s winning moves. However, simulations of the search while varying the shutter size, complexity levels, noise levels, branching factor, and computational limitations indicate that despite its costs, a narrow shutter strategy is the dominant strategy for most of the parameter space. Finally, we show that in the presence of computational limitations, the shutter heuristic enhances the performance of deep learning networks in these end-game scenarios. Together, our findings suggest a novel adaptive heuristic that benefits search in a vast space of possibilities of a strategic game.     

Eukaryotic Initiation Factor 2α - a Downstream Effector of Mammalian Target of Rapamycin - Modulates DNA Repair and Cancer Response to Treatment

In an effort to circumvent resistance to rapamycin – an mTOR inhibitor - we searched for novel rapamycin-downstream-targets that may be key players in the response of cancer cells to therapy. We found that rapamycin, at nM concentrations, increased phosphorylation of eukaryotic initiation factor (eIF) 2α in rapamycin-sensitive and estrogen-dependent MCF-7 cells, but had only a minimal effect on eIF2α phosphorylation in the rapamycin-insensitive triple-negative MDA-MB-231 cells. Addition of salubrinal – an inhibitor of eIF2α dephosphorylation – decreased expression of a surface marker associated with capacity for self renewal, increased senescence and induced clonogenic cell death, suggesting that excessive phosphorylation of eIF2α is detrimental to the cells'' survival. Treating cells with salubrinal enhanced radiation-induced increase in eIF2α phosphorylation and clonogenic death and showed that irradiated cells are more sensitive to increased eIF2α phosphorylation than non-irradiated ones. Similar to salubrinal - the phosphomimetic eIF2α variant - S51D - increased sensitivity to radiation, and both abrogated radiation-induced increase in breast cancer type 1 susceptibility gene, thus implicating enhanced phosphorylation of eIF2α in modulation of DNA repair. Indeed, salubrinal inhibited non-homologous end joining as well as homologous recombination repair of double strand breaks that were induced by I-SceI in green fluorescent protein reporter plasmids. In addition to its effect on radiation, salubrinal enhanced eIF2α phosphorylation and clonogenic death in response to the histone deacetylase inhibitor – vorinostat. Finally, the catalytic competitive inhibitor of mTOR - Ku-0063794 - increased phosphorylation of eIF2α demonstrating further the involvement of mTOR activity in modulating eIF2α phosphorylation. These experiments suggest that excessive phosphorylation of eIF2α decreases survival of cancer cells; making eIF2α a worthy target for drug development, with the potential to enhance the cytotoxic effects of established anti-neoplastic therapies and circumvent resistance to rapalogues and possibly to other drugs that inhibit upstream components of the mTOR pathway.     

Optimal growth temperature of prokaryotes correlates with class II amino acid composition

Partitioning of aminoacyl-tRNA synthetases and their associated amino acids into two classes allows us to distinguish between thermophilic and mesophilic species based only on amino acids composition. The CLASSDB program has been developed for amino acid content analysis in organisms treated individually or pooled together to form a pattern of characteristic properties. A strong correlation has been observed between optimal growth temperature (OGT) of organisms and class II amino acids content. Amino acid composition in organisms closely related phylogenetically but dissimilar in their OGT testifies that thermo-adaptation happens rather rapidly on the time scale of evolution.     

Using bleach-chase to measure protein half-lives in living cells

Protein removal has a central role in numerous cellular processes. Obtaining systematic measurements of multiple protein removal rates is necessary to understand the principles that govern these processes, but it is currently a major technical challenge. To address this, we developed 'bleach-chase', a noninvasive method for measuring the half-lives of multiple proteins at high temporal resolution in living cells. The method uses a library of annotated human reporter cell clones, each with a unique fluorescently tagged protein expressed from its native chromosomal location. In this protocol, we detail a simple procedure that bleaches the cells and uses time-lapse fluorescence microscopy and automated image analysis to systematically measure the half-life dynamics of multiple proteins. The duration of the protocol is 4-5 d. The method may be applicable to a wide range of fluorescently tagged proteins and cell lines.     

Type Six Secretion System of Bordetella bronchiseptica and Adaptive Immune Components Limit Intracellular Survival During Infection

The Type Six Secretion System (T6SS) is required for Bordetella bronchiseptica cytotoxicity, cytokine modulation, infection, and persistence. However, one-third of recently sequenced Bordetella bronchiseptica strains of the predominantly human-associated Complex IV have lost their T6SS through gene deletion or degradation. Since most human B. bronchiseptica infections occur in immunocompromised patients, we determine here whether loss of Type Six Secretion is beneficial to B. bronchiseptica during infection of immunocompromised mice. Infection of mice lacking adaptive immunity (Rag1^-/- mice) with a T6SS-deficient mutant results in a hypervirulent phenotype that is characterized by high numbers of intracellular bacteria in systemic organs. In contrast, wild-type B. bronchiseptica kill their eukaryotic cellular hosts via a T6SS-dependent mechanism that prevents survival in systemic organs. High numbers of intracellular bacteria recovered from immunodeficient mice but only low numbers from wild-type mice demonstrates that B. bronchiseptica survival in an intracellular niche is limited by B and T cell responses. Understanding the nature of intracellular survival during infection, and its effects on the generation and function of the host immune response, are important to contain and control the spread of Bordetella-caused disease.