Synthesis and Properties of P1, P2-, P1, P3- and P1, P4-Dinucleoside Di-, Tri- and Tetraphosphate mRNA 5′-Cap Analogues

Abstract

Chemically synthesized dinucleoside P¹, P²-di-, P¹, P³-tri- and P¹, P⁴-tetraphosphates, derivatives of 5′-linked 7-methylguanosine and guanosine were characterized with respect to their structural properties and functional effect on eukaryotic translation inhibition.     

Dissecting a role of a charge and conformation of Tat2 peptide in allosteric regulation of 20S proteasome

Proteasome is a ‘proteolytic factory’ that constitutes an essential part of the ubiquitin‐proteasome pathway. The involvement of proteasome in regulation of all major aspects of cellular physiology makes it an attractive drug target. So far, only inhibitors of the proteasome entered the clinic as anti‐cancer drugs. However, proteasome regulators may also be useful for treatment of inflammatory and neurodegenerative diseases. We established in our previous studies that the peptide Tat2, comprising the basic domain of HIV‐1 Tat protein: R⁴⁹KKRRQRR⁵⁶, supplemented with Q⁶⁶DPI⁶⁹ fragment, inhibits the 20S proteasome in a noncompetitive manner. Mechanism of Tat2 likely involves allosteric regulation because it competes with the proteasome natural 11S activator for binding to the enzyme noncatalytic subunits. In this study, we performed alanine walking coupled with biological activity measurements and FTIR and CD spectroscopy to dissect contribution of a charge and conformation of Tat2 to its capability to influence peptidase activity of the proteasome. In solution, Tat2 and most of its analogs with a single Ala substitution preferentially adopted a conformation containing PPII/turn structural motifs. Replacing either Asp10 or two or more adjacent Arg/Lys residues induced a random coil conformation, probably by disrupting ionic interactions responsible for stabilization of the peptides ordered structure. The random coil Tat2 analogs lost their capability to activate the latent 20S proteasome. In contrast, inhibitory properties of the peptides more significantly depended on their positive charge. The data provide valuable clues for the future optimization of the Tat2‐based proteasome regulators. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

Ovarian nests in cultured Russian sturgeon Acipenser gueldenstaedtii and North American paddlefish Polyodon spathula comprised of previtellogenic oocytes

Ovarian nests in the ovaries of sexually maturing Russian sturgeon Acipenser gueldenstaedtii and North American paddlefish Polyodon spathula were investigated. They comprised early previtellogenic, diplotene stage oocytes and somatic cells. In the nucleoplasm, these oocytes contained chromatin in the form of grains, threads and lampbrush chromosomes, primary nucleoli and multiple nucleoli. Two stages of oocytes in nests were distinguished by differences in the distribution of mitochondria with distorted cristae and lipid droplets in the ooplasm. These stages were as follows: pre‐early stage 1 (PE 1) and early stage 1 (EP 1) previtellogenic oocytes. In PE 1 oocytes few mitochondria with distorted cristae and lipid droplets were distributed randomly. The ooplasm of PE 1 oocytes was not differentiated into homogeneous and granular compartments. In EP 1 oocytes, mitochondria with distorted cristae were more numerous and grouped in the vicinity of the nucleus, lipid droplets accumulated near these mitochondria. In the nucleoplasm of EP 1 oocytes several low electron‐dense spherical bodies, possibly Cajal bodies, were present.     

Nuage morphogenesis becomes more complex: two translocation pathways and two forms of nuage coexist in Drosophila germline syncytia

We have developed a simple and reliable method of preserving antigen immunoreactivity with concomitant excellent retention of the cell ultrastructure. Using this method, we have been able to follow the origin and developmental stages of nuage accumulations within the nurse cell/oocyte syncytium in the ovary of the fruit fly, Drosophila melanogaster, at the ultrastructural level. We have found two morphologically and biochemically distinct forms of nuage material in the nurse cell cytoplasm: translocating accumulations of nuage containing the Vasa protein, termed sponge bodies and stationary polymorphic accumulations of nuage enriched in Argonaute and Survival of motor neuron proteins. Immunogold labeling combined with confocal fluorescent and ultrastructural analyses have revealed that the Vasa-containing nuage accumulations remain closely associated with the cisternae of the endoplasmic reticulum throughout their lifetimes. The migration mechanism of the Vasa-positive nuage appears distinct from the microtubule-dependent translocation of oskar ribonucleoprotein complexes. We postulate that these two distinct nuage translocation pathways converge in the formation of the polar granules within the polar/germ plasm of the oocyte posterior pole. We also provide morphological and immunocytochemical evidence that these polymorphic nuage accumulations correspond to the recently described cytoplasmic domains termed U body-P body complexes.     

Synthesis of cis-(1-->3)-glycosides of allyl 2-acetamido-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranoside

Syntheses of allyl 2,3,4-tri-O-benzyl-alpha-D-gluco- and D-galactopyranosyluronate-(1-->3)-2-acetamido-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranoside via oxidation of the hydroxymethyl group of allyl 2,3,4-tri-O-benzyl-alpha-D-gluco- and D-galactopyranosyl-(1-->3)-2-acetamido-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranoside under Jones conditions are described. Structures of the title compounds were confirmed by (1)H and (13)C NMR spectroscopy.     

Composition and distribution of meiofauna,including nematode genera,in two contrasting Arctic beaches

The meiofauna of two tidal beaches, one exposed and one more sheltered, on Bjornoya (Bear Island) was investigated in summer 2000. Both meiofaunal densities and composition seem to be controlled by physical properties of the sediment, which in turn are controlled by exposure. The moderately and poorly sorted sediments in the sheltered beach were more abundant in terms of meiofaunal densities than the well sorted sediments in the exposed beach (254–481 individuals in 10 cm² vs 7–269 individuals in 10 cm², respectively). In total, seven higher meiofaunal taxa were found. Turbellaria were the numerically dominant taxon in the exposed beach. In the sheltered beach, Turbellaria also dominated, followed by Nematoda and Harpacticoida. The vertical distribution of the meiofauna was in accordance with what has been reported from other intertidal beaches. Nematoda were studied in detail and their densities ranged over 0.7–7.7 individuals in 10 cm² in the exposed beach and 2.7–186.0 individuals in 10 cm² in the sheltered beach. Nematodes were identified to genus level and a total of eight nematode genera were found. Sediment community respiration, measured as oxygen consumption, ranged between 2.3 cm³ O₂ m^–2 h^–1 in the exposed beach and 7.3 cm³ O₂ m^–2 h^–1 in the sheltered beach (respectively, the equivalent of 24 mg and 75 mg of organic carbon metabolised per day). Values from the sheltered site are within the range of results registered in much warmer localities.     

Direct analysis of nematode cis- and trans-spliceosomes: a functional role for U5 snRNA in spliced leader addition trans-splicing and the identification of novel Sm snRNPs.

Most nuclear pre-mRNAs in nematodes are processed by both cis- and trans-splicing. In trans-splicing, the 5' terminal exon, the spliced leader sequence (SL), is derived from a trans-splicing specific Sm snRNP, the SL RNP. Because U snRNPs are required cofactors for trans-splicing, and because this processing reaction proceeds via a two-step reaction pathway identical to that of cis-splicing, it has long been assumed that trans-splicing is catalyzed in a complex analogous to the cis-spliceosome. However, similarities or differences between cis- and trans-spliceosomes have not been established. In particular, the role of U5 snRNP in trans-splicing has been unclear. Here, we have used affinity selection to analyze the U snRNA constituents of nematode cis- and trans-spliceosomes. We find that U5 snRNP is an integral component of the trans-spliceosome and, using site-specific crosslinking, we show that U5 snRNP establishes specific Interactions with the SL RNA exon. We also identify two novel Sm snRNPs that are enriched in both cis- and trans-spliceosomes. Finally, we provide evidence that a SL RNP-containing multi-snRNP (SL, U4, U5, and U6 RNPs) may be a functional precursor in trans-spliceosome assembly.     

Impairment of the rod outer segment membrane guanylate cyclase dimerization in a cone-rod dystrophy results in defective calcium signaling

Rod outer segment membrane guanylate cyclase1 (ROS-GC1) is the original member of the membrane guanylate cyclase subfamily whose distinctive feature is that it transduces diverse intracellularly generated Ca(2+) signals in the sensory neurons. In the vertebrate retinal neurons, ROS-GC1 is pivotal for the operations of phototransduction and, most likely, of the synaptic activity. The phototransduction- and the synapse-linked domains are separate, and they are located in the intracellular region of ROS-GC1. These domains sense Ca(2+) signals via Ca(2+)-binding proteins. These proteins are ROS-GC activating proteins, GCAPs. GCAPs control ROS-GC1 activity through two opposing regulatory modes. In one mode, at nanomolar concentrations of Ca(2+), the GCAPs activate the cyclase and as the Ca(2+) concentrations rise, the cyclase is progressively inhibited. This mode operates in phototransduction via two GCAPs: 1 and 2. The second mode occurs at micromolar concentrations of Ca(2+) via S100beta. Here, the rise of Ca(2+) concentrations progressively stimulates the enzyme. This mode is linked with the retinal synaptic activity. In both modes, the final step in Ca(2+) signal transduction involves ROS-GC dimerization, which causes the cyclase activation. The identity of the dimerization domain is not known. A heterozygous, triple mutation -E786D, R787C, T788M- in ROS-GC1 has been connected with autosomal cone-rod dystrophy in a British family. The present study shows the biochemical consequences of this mutation on the phototransduction- and the synapse-linked components of the cyclase. (1) It severely damages the intrinsic cyclase activity. (2) It significantly raises the GCAP1- and GCAP2-dependent maximal velocity of the cyclase, but this compensation, however, is not sufficient to override the basal cyclase activity. (3) It converts the cyclase into a form that only marginally responds to S100beta. The mutant produces insufficient amounts of the cyclic GMP needed to drive the machinery of phototransduction and of the retinal synapse at an optimum level. The underlying cause of the breakdown of both types of machinery is that, in contrast to the native ROS-GC1, the mutant cyclase is unable to change from its monomeric to the dimeric form, the form required for the functional integrity of the enzyme. The study defines the CORD in molecular terms, at a most basic level identifies a region that is critical in its dimer formation, and, thus, discloses a single unifying mechanistic theme underlying the complex pathology of the disease.     

Hydrolysis of some mRNA 5'-cap analogs catalyzed by the human Fhit protein--and lupin ApppA hydrolases.

Hydrolysis of the following four cap analogs: m7G(5')ppp(5')A, m7G(5')ppp(5')m6A, m7G(5')ppp(5')m2'OG and m7G(5')ppp(5')2'dG catalyzed by homogeneous human Fhit protein and yellow lupin Ap3A hydrolase has been investigated. The hydrolysis products were identified by HPLC analysis and the K(m) and Vmax values calculated based on the data obtained by the fluorimetric method.