The E3 Ubiquitin-Ligase Bmi1/Ring1A Controls the Proteasomal Degradation of Top2α Cleavage Complex – A Potentially New Drug Target

Background

The topoisomerases Top1, Top2α and Top2β are important molecular targets for antitumor drugs, which specifically poison Top1 or Top2 isomers. While it was previously demonstrated that poisoned Top1 and Top2β are subject to proteasomal degradation, this phenomena was not demonstrated for Top2α.

Methodology/Principal Findings

We show here that Top2α is subject to drug induced proteasomal degradation as well, although at a lower rate than Top2β. Using an siRNA screen we identified Bmi1 and Ring1A as subunits of an E3 ubiquitin ligase involved in this process. We show that silencing of Bmi1 inhibits drug-induced Top2α degradation, increases the persistence of Top2α-DNA cleavage complex, and increases Top2 drug efficacy. The Bmi1/Ring1A ligase ubiquitinates Top2α in-vitro and cellular overexpression of Bmi1 increases drug induced Top2α ubiquitination. A small-molecular weight compound, identified in a screen for inhibitors of Bmi1/Ring1A ubiquitination activity, also prevents Top2α ubiquitination and drug-induced Top2α degradation. This ubiquitination inhibitor increases the efficacy of topoisomerase 2 poisons in a synergistic manner.

Conclusions/Significance

The discovery that poisoned Top2α is undergoing proteasomal degradation combined with the involvement of Bmi1/Ring1A, allowed us to identify a small molecule that inhibits the degradation process. The Bmi1/Ring1A inhibitor sensitizes cells to Top2 drugs, suggesting that this type of drug combination will have a beneficial therapeutic outcome. As Bmi1 is also a known oncogene, elevated in numerous types of cancer, the identified Bmi1/Ring1A ubiquitin ligase inhibitors can also be potentially used to directly target the oncogenic properties of Bmi1.     

Phylo SI: a new genome-wide approach for prokaryotic phylogeny

The evolutionary history of all life forms is usually represented as a vertical tree-like process. In prokaryotes, however, the vertical signal is partly obscured by the massive influence of horizontal gene transfer (HGT). The HGT creates widespread discordance between evolutionary histories of different genes as genomes become mosaics of gene histories. Thus, the Tree of Life (TOL) has been questioned as an appropriate representation of the evolution of prokaryotes. Nevertheless a common hypothesis is that prokaryotic evolution is primarily tree-like, and a routine effort is made to place new isolates in their appropriate location in the TOL. Moreover, it appears desirable to exploit non–tree-like evolutionary processes for the task of microbial classification. In this work, we present a novel technique that builds on the straightforward observation that gene order conservation (‘synteny’) decreases in time as a result of gene mobility. This is particularly true in prokaryotes, mainly due to HGT. Using a ‘synteny index’ (SI) that measures the average synteny between a pair of genomes, we developed the phylogenetic reconstruction tool ‘Phylo SI’. Phylo SI offers several attractive properties such as easy bootstrapping, high sensitivity in cases where phylogenetic signal is weak and computational efficiency. Phylo SI was tested both on simulated data and on two bacterial data sets and compared with two well-established phylogenetic methods. Phylo SI is particularly efficient on short evolutionary distances where synteny footprints remain detectable, whereas the nucleotide substitution signal is too weak for reliable sequence-based phylogenetic reconstruction. The method is publicly available at http://research.haifa.ac.il/ssagi/software/PhyloSI.zip.     

Maximum likelihood Jukes-Cantor triplets: analytic solutions

Maximum likelihood (ML) is a popular method for inferring a phylogenetic tree of the evolutionary relationship of a set of taxa, from observed homologous aligned genetic sequences of the taxa. Generally, the computation of the ML tree is based on numerical methods, which in a few cases, are known to converge to a local maximum on a tree, which is suboptimal. The extent of this problem is unknown, one approach is to attempt to derive algebraic equations for the likelihood equation and find the maximum points analytically. This approach has so far only been successful in the very simplest cases, of three or four taxa under the Neyman model of evolution of two-state characters. In this paper we extend this approach, for the first time, to four-state characters, the Jukes-Cantor model under a molecular clock, on a tree T on three taxa, a rooted triple. We employ spectral methods (Hadamard conjugation) to express the likelihood function parameterized by the path-length spectrum. Taking partial derivatives, we derive a set of polynomial equations whose simultaneous solution contains all critical points of the likelihood function. Using tools of algebraic geometry (the resultant of two polynomials) in the computer algebra packages (Maple), we are able to find all turning points analytically. We then employ this method on real sequence data and obtain realistic results on the primate-rodents divergence time.     

Characterization of sodium currents in mammalian sensory neurons cultured in serum-free defined medium with and without nerve growth factor

Summary The influence of nerve growth factor (NGF) on Na currents of rat dorsal root ganglia (DRG) was studied in neurons obtained from newborns and cultured for 2–30 hr inserum-free defined medium (SFM). Cell survival for the period studied was 78–87% both with and without NGF. Na currents were detected in all cells cultured for 6–9 hr. They were also detected after 2 hr in culture in 21.5% of the cells cultured without NGF (–NGF cells), and in 91.5% of the cells cultured with NGF (+NGF cells). Current density of the -NGF cells was 2.3 and 2 pA/m² after growth for 2 and 6–9 hr, respectively, compared to 3.0 and 3.9 pA/m² for the +NGF cells. The +NGF cells were separated into fast (F), Intermediate (I) and slow (S) cells, based on the Na current they expressed, while -NGF cells were all of theI type.F, I andS currents differed in their voltage-dependent inactivation (Vh ₅₀=–79, –28 and –20 mV), kinetics of inactivation (tau _h =0.55, 1.3 and 7.75 msec), and TTX sensitivity (K _i=60, 550 and 1100nm). All currents were depressed by [Ca] _o with aKd _Ca of 22, 17 and 8mm forF, I andS currents, respectively. Current density ofF andS currents was 5.5 and 5 pA/m² for theI current. The concentration-dependent curve ofI currentvs. TTX indicated thatI current has two sites: one withF-like and another withS-likeK _i for TTX. Hybridization ofF andS currents yieldI-like currents. Thus, the major effect of NGF on Na currents in SFM is the accleration of Na current acquisition and diversity, reflected in an increase of either theS orF type in a cell.     

Peroxidase and catalase activity in leaves of Halimione portulacoides exposed to salinity

The effect of high NaCl concentrations on the activity of catalase (EC 1.11.1.6), peroxidase (EC 1.11.1.7) and malate dehydrogenase (NAD⁺-linked; EC 1.1.1.37) from leaves of Halimione portulacoides (L.) Aellen was studied. The plants were exposed to high salinity during growth and enzyme activity was measured either in the absence or in the presence of various concentrations of NaCl. Increasing salinity in vitro induced three types of effects: (1) an increase in activity (peroxidase); (2) a decrease in activity (catalase); (3) stimulation by low salt concentration but inhibition by higher concentrations (malate dehydrogenase). Salinity in vivo induced a marked decrease in catalase and malate dehydrogenase activities. However, peroxidase in vivo showed an optimum curve of activity vs external NaCl concentration, with an optimum at ca 1 M NaCl. Exposure of plants to salinity induced changes in the properties of the enzyme proteins: they precipitated at a higher (NH₄)₂SO₄ concentration, were eluted later during Sephadex G-200 filtration, and showed a shift in the maximal, minimal and optimal temperatures. These data are interpreted as evidence for conformational changes in the enzymes due to prolonged exposure to high salinity stress; such changes could be disruption into monomers (catalase and malate dehydrogenase), or changes in molecular shape (in the peroxidase).     

Phorbol ester prevents the thyroid-stimulating-hormone-induced but not the forskolin-induced decrease of cAMP-dependent protein kinase activity in thyroid cell cultures

The potent tumor promoter 12-O-tetradecanoyl-phorbol 13-acetate (TPA) affects several thyroid cell functions and interacts with thyroid-stimulating hormone (TSH) either by inhibiting or potentiating its action on different cellular parameters. Since phorbol ester acts mainly through the activation of protein kinase C, which is its receptor, we studied this activation and its interaction with TSH and forskolin in suspension cultures of porcine thyroid cells. In thyroid cell cultures, TPA has a dual effect on protein kinase C activity: immediately (2-5 min) after exposure of cells to TPA, it began to be translocated from the cytosol to the particulate fraction. The transfer of the cytosolic enzyme was total and could occur with or without a loss of activity. The translocated enzyme still needed Ca2+ and phospholipids for its activation. The basal activity increased transiently (2-4 h) in both the cytosol and particulate fractions during translocation. The peak activity in the particulate fraction was reached 10-30 min after exposure of cells to TPA, and was followed by down-regulation of protein kinase C and almost complete disappearance of its activity. The residual activity was about 13% of control after a 2-day exposure to TPA. It was unequally distributed between cytosol (4%) and particulate fraction (9%). Prolonged exposure of cells to TPA did not affect either the activity or the subcellular distribution of the cAMP-dependent protein kinase activity. TPA interacted with TSH and prevented the decrease of this activity induced by prolonged exposure of cells to the hormone not only when it was introduced simultaneously with TSH, but also when it was added 24 h after TSH. However, the forskolin-induced decrease in cAMP-dependent protein kinase activity was not prevented by the presence of TPA. TPA also affected the increases in cAMP accumulation mediated by TSH and forskolin. The TSH-induced increase was significantly stimulated by TPA after short contacts (5-15 min), while longer preincubations of cells with TPA provoked a very strong inhibition of the TSH action. However, the forskolin-induced stimulation of the cAMP accumulation was maintained and even further increased in the presence of TPA. Consequently, the actions of TSH and TPA are apparently interdependent, while those of forskolin and TPA seem to be parallel and independent. Neither TSH nor forskolin prevented the TPA-induced down regulation of protein kinase C. The biologically inactive phorbol ester analogue 4 alpha-phorbol 12,13-didecanoate had no effect on protein kinase C activity, and did not interact with either TSH or forskolin.(ABSTRACT TRUNCATED AT 400 WORDS)     

Persistent activity in neural networks with dynamic synapses

Persistent activity states (attractors), observed in several neocortical areas after the removal of a sensory stimulus, are believed to be the neuronal basis of working memory. One of the possible mechanisms that can underlie persistent activity is recurrent excitation mediated by intracortical synaptic connections. A recent experimental study revealed that connections between pyramidal cells in prefrontal cortex exhibit various degrees of synaptic depression and facilitation. Here we analyze the effect of synaptic dynamics on the emergence and persistence of attractor states in interconnected neural networks. We show that different combinations of synaptic depression and facilitation result in qualitatively different network dynamics with respect to the emergence of the attractor states. This analysis raises the possibility that the framework of attractor neural networks can be extended to represent time-dependent stimuli.     

A comparative evaluation of presence-only methods for modelling species distribution

In spite of increasing application of presence-only models in ecology and conservation and the growing number of such models, little is known about the relative performance of different modelling methods, and some of the leading models (e.g. GARP and ENFA) have never been compared with one another. Here we compare the performance of six presence-only models that have been selected to represent an increasing level of model complexity [BIOCLIM, HABITAT, Mahalanobis distance (MD), DOMAIN, ENFA, and GARP] using data on the distribution of 42 species of land snails, nesting birds, and insectivorous bats in Israel. The models were calibrated using data from museum collections and observation databases, and their predictions were evaluated using Cohen's Kappa based on field data collected in a standardized sampling design covering most parts of Israel. Predictive accuracy varied between modelling methods with GARP and MD showing the highest accuracy, BIOCLIM and ENFA showing the lowest accuracy, and HABITAT and DOMAIN showing intermediate accuracy levels. Yet, differences between the various models were relatively small except for GARP and MD that were significantly more accurate than BIOCLIM and ENFA. In spite of large differences among species in prevalence and niche width, neither prevalence nor niche width interacted with the modelling method in determining predictive accuracy. However, species with relatively narrow niches were modelled more accurately than species with wider niches. Differences among species in predictive accuracy were highly consistent over all modelling methods, indicating the need for a better understanding of the ecological and geographical factors that influence the performance of species distribution models.     

Cellular localization and phosphorylation of Hrb1p is independent of Sky1p

Protein phosphorylation plays a major role in regulating cellular functions. We have previously demonstrated that Sky1p, the SR protein kinase of the budding yeast Saccharomyces cerevisiae, is a regulator of polyamine transport and ion homeostasis. Since its kinase activity was demonstrated essential for fulfilling these roles, we assumed that Sky1p function via substrates phosphorylation. Using an in vitro phosphorylation assay, we have identified Hrb1p as a putative Sky1p substrate. However, phosphorylation analysis in WT and sky1Delta cells and localization studies disproved Hrb1p as a true Sky1p substrate, although a segment of the RS domain is required for determining its subcellular localization. Furthermore, we demonstrate that Hrb1p and additional putative Sky1p substrates, identified by computational approach, are not involved in mediating the spermine tolerant phenotype of sky1Delta cells.