Topological frame extension

The concept of nearness on a set was introduced by H. Herrlich. D. Le- seberg generalized nearness by introducing supernearness, which generalizes also supertopology as de ned by D. Doitchinov. In this paper, our work is based on the representation theorem of M. H. Stone and the de nition of nearness. We de ne proximity and nearness on a Boolean frame and then, by using these, we de ne supertopic frame, supernear frame and paranear frame. We study basic properties of the concepts de ned. We also introduce a topological extension on a Boolean frame and investigate its behavior

Architecture of coatomer: Molecular characterization of delta-COP and protein interactions within the complex

Copyright © 2011 by The Rockefeller University Press.Coatomer is a cytosolic protein complex that forms the coat of COP I-coated transport vesicles. In our attempt to analyze the physical and functional interactions between its seven subunits (coat proteins, [COPs] alpha-zeta), we engaged in a program to clone and characterize the individual coatomer subunits. We have now cloned, sequenced, and overexpressed bovine alpha-COP, the 135-kD subunit of coatomer as well as delta-COP, the 57-kD subunit and have identified a yeast homolog of delta-COP by cDNA sequence comparison and by NH2-terminal peptide sequencing. delta-COP shows homologies to subunits of the clathrin adaptor complexes AP1 and AP2. We show that in Golgi-enriched membrane fractions, the protein is predominantly found in COP I-coated transport vesicles and in the budding regions of the Golgi membranes. A knock-out of the delta-COP gene in yeast is lethal. Immunoprecipitation, as well as analysis exploiting the two-hybrid system in a complete COP screen, showed physical interactions between alpha- and epsilon-COPs and between beta- and delta-COPs. Moreover, the two-hybrid system indicates interactions between gamma- and zeta-COPs as well as between alpha- and beta' COPs. We propose that these interactions reflect in vivo associations of those subunits and thus play a functional role in the assembly of coatomer and/or serve to maintain the molecular architecture of the complex.This work was supported by The Deutsche Forschungsgemeinschaft (SFB 352), the Human Frontier Science Program, and the Swiss National Science Foundation No. 31-43366.95

Investigating the regulation of AMP-activated protein kinase and SNF1

AMP-activated protein kinase (AMPK) has long been known to play a critical role in the maintenance of energy homeostasis through direct interaction with or altering gene and protein expression of key players in diverse metabolic pathways. AMPK has been implicated in a number of diseases with roots in metabolic dysregulation, including obesity, type 2 diabetes and cancer. Elucidating the regulation of AMPK is an important part in understanding the progression of these diseases, and for developing small molecule modulators of AMPK activity which could have therapeutic applications. AMPK activity is determined by the phosphorylation status of T172 in the activation loop of the α subunit kinase domain. Binding of AMP to the γ subunit also increases its activity, primarily by preventing dephosphorylation of T172 but also by direct allosteric activation of the complex. The overall aim of this study was to investigate nucleotide regulation of AMPK. Site-directed mutagenesis studies showed that loss of highly conserved residues in γ1 disrupts regulation of both dephosphorylation and allosteric activation of AMPK by AMP. However, my studies revealed that these mutations do not have site-specific effects. The role of ADP in AMPK regulation was also investigated following the observation that this nucleotide also prevented dephosphorylation and inactivation of AMPK. The action of ADP on AMPK activity was characterised in wild-type complexes and insights from new structures of the active AMPK complex has provided insight into the molecular mechanism underlying AMP/ADP protection and dephosphorylation of T172. The yeast homologue of AMPK, SNF1, plays a central role in responding to glucose limitation and adaption to alternative carbon sources. Recombinant SNF1 complexes were used to show that ADP is the long-sought metabolite responsible for transmitting this low glucose signal and activates SNF1 by a similar mechanism to that seen in AMPK, preventing dephosphorylation and inactivation. Together these studies identify an important activator of both AMPK and SNF1, drawing parallels between these two systems and characterising a highly conserved regulatory mechanism, suggesting that ADP may represent a unifying trigger for activation of AMPK homologues in diverse species. Finally a potential link between AMPK and redox metabolism was identified in the form of NADH, opening new avenues of research in this field

CBS domains form energy-sensing modules whose binding of adenosine ligands is disrupted by disease mutations

CBS domains are defined as sequence motifs that occur in several different proteins in all kingdoms of life. Although thought to be regulatory, their exact functions have been unknown. However, their importance was underlined by findings that mutations in conserved residues within them cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): Wolff-Parkinson-White syndrome (γ2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members); and homocystinuria (cystathionine β-synthase). AMP-activated protein kinase is a sensor of cellular energy status that is activated by AMP and inhibited by ATP, but the location of the regulatory nucleotide-binding sites (which are prime targets for drugs to treat obesity and diabetes) was not characterized. We now show that tandem pairs of CBS domains from AMP-activated protein kinase, IMP dehydrogenase-2, the chloride channel CLC2, and cystathionine β-synthase bind AMP, ATP, or S-adenosyl methionine,while mutations that cause hereditary diseases impair this binding. This shows that tandem pairs of CBS domains act, in most cases, as sensors of cellular energy status and, as such, represent a newly identified class of binding domain for adenosine derivatives

Arabidopsis SCF-SnRK ubiquitin-ligáz komplexek szerkezetének vizsgálata és az alegységek funkcionális analízise = Study of the subunit structure of Arabidopsis SCF-SnRK ubiquitin ligase complexes and functional analysis of the subunits

Az Arabidopsis SnRK heterotrimer kináz komplex epitópjelölt alegységeinek szuszpenziós sejtkultúrában és növényekben való expressziójával a komplexek alegységszerkezetét és kölcsönhatásait vizsgáltuk. Megállapítottuk, ha a katalitikus AKIN10/11 kináz alegység a PRL1 inhibítor fehérjével való asszociációnak köszönhetoen inaktív, nem foszforilált formában van, akkor kölcsönhat a 26S proteaszómával de ekkor az AKINb és g regulátor alegységek jelenléte nem detektálható. Az AKIN-PRL1 kapcsolat hiánya illetve disszociációja az AKIN10/11 alegység autofoszforilálását és aktiválását eredményezi, ekkor a 26S proteaszóma mellett az AKINb és g alegységek valamint a COP9 szignaloszóma is a komplex részét képezi. Ismert, hogy a COP9 szignaloszóma az SCF E3 ubiquitin ligáz komplexeket inaktiválja a kullin alegység deneddylálása révén. Az általunk javasolt modell feltételezi, hogy az SnRK-COP9 kölcsönhatás gátolja a deneddilációt, ezáltal aktiválja az SCF komplexeket, és elosegíti az aktivált SCF-szubsztrát komplexek 26S proteaszómához való dokkolását. | We investigated the subunit structure and interactions of the heterotrimeric SnRK kinase complex by expressing epitope-tagged subunits in Arabidopsis plants and cultured cells. When the catalytic AKIN10/11 kinase subunit is kept in an unphosphorylated inactive form through association with the inhibitor PRL1 protein, the catalytic subunit interacts with the 26S proteasome but the presence of AKINb and g regulatory subunits cannot be detected in the complex. Dissociation of the AKIN-PRL1 interaction, or the lack of it, results in phosphorylation and activation of the AKIN10/11 subunit which then binds to the 26S proteasome as well as to the AKINb and g subunits and recruits COP9 signalosome to the holoenzyme complex. It is known that due to its cullin deneddylase activity the COP9 signalosome inactivates SCF E3 ubiquitin ligase complexes. Our results suggest a model in which the SnRK-COP9 interaction abolishes the deneddylase activity of COP9 and results in the formation of active SCF-substrate complexes and might facilitate their docking to the 26S proteasome

Surface-layer formation by reductive decomposition of LiPF6 at relatively high potentials on negative electrodes in lithium ion batteries and its suppression

In using a LiPF6/ethylene carbonate–dimethyl carbonate electrolyte for lithium ion batteries (LIBs), a certain reductive reaction is known to occur at a relatively high potential (ca. 2.6 V vs. Li[+]/Li) on Sn electrode, but its details are still unknown. By means of in-situ X-ray reflectometry, X-ray photoelectron spectroscopy, scanning electron microscopy observations and electrochemical measurements (by using mainly Sn electrode, and additionally Pt, graphite electrodes), we have found out that this reduction eventually forms an inactive passivation-layer consisting mainly of insulative LiF ascribed to the reductive decomposition of LiPF6, which significantly affects the battery cyclability. In contrast, a solid-electrolyte interphase (SEI) is formed by the reductive reaction of the solvent at ca. 1.5 V vs. Li[+]/Li, which is lower than the reduction potential of LiPF6. However, we have found that the formation of SEI preempts that of the passivation layer when holding the electrode at a potential lower than 1.5 V vs. Li[+]/Li. Consequently, the cyclability is improved by suppressing the formation of the inactive passivation layer. Such a pretreatment would be quite effective on improvement of the battery cyclability, especially for a relatively noble electrode whose oxidation potential is between 1.5 V and 2.6 V vs. Li[+]/Li

Studies of molecular mechanisms integrating carbon metabolism and growth in plants

Plants use light energy, carbon dioxide and water to produce sugars and other carbohydrates, which serve as stored energy reserves and as building blocks for biosynthetic reactions. Supply of light is variable and plants have evolved means to adjust their growth and development accordingly. An increasing body of evidence suggests that the basic mechanisms for sensing and signaling energy availability in eukaryotes are evolutionary conserved and thus shared between plants, animals and fungi. I have used different experimental approaches that take advantage of findings from other eukaryotes in studying carbon and energy metabolism in plants. In the first part, I developed a novel screening procedure in yeast aimed at isolating cDNAs from other organisms encoding proteins with a possible function in sugar sensing or signaling. The feasibility of the method was confirmed by the cloning of a cDNA from Arabidopsis thaliana encoding a new F-box protein named AtGrh1, which is related to the yeast Grr1 protein that is involved in glucose repression. In the second part of the study, plant homologues of key components in the yeast glucose repression pathway were cloned and characterized in the moss Physcomitrella patens, in which gene function can be studied by gene targeting. We first cloned PpHXK1 which was shown to encode a chloroplast localized hexokinase representing a previously overlooked class of plant hexokinases with an N-terminal chloroplast transit peptide. Significantly, PpHxk1 is the major hexokinase in Physcomitrella, accounting for 80% of the glucose phosphorylating activity. A knockout mutant deleted for PpHXK1 exhibits a complex phenotype affecting growth, development and sensitivities to plant hormones. I also cloned and characterized two closely related Physcomitrella genes, PpSNF1a and PpSNF1b, encoding type 1 Snf1-related kinases. A double knockout mutant for these genes was viable even though it lacks detectable Snf1-like kinase activity. The mutant suffers from pleiotropic phenotypes which may reflect a constitutive high energy growth mode. Significantly, the double mutant requires constant high light and is therefore unable to grow in a normal day/night light cycle. These findings are consistent with the proposed role of the Snf1-related kinases as energy gauges which are needed to recognize and respond to low energy conditions