Transterm: a database of messenger RNA components and signals

Transterm facilitates studies of messenger RNAs and translational control signals. Each messenger RNA (mRNA) from GenBank is extracted and broken into its functional components, its coding sequence, initiation context, termination context, flanking sequence representing its 5' UTR (untranslated region), 3' UTR and translational signals. In addition, numerical parameters characterising each coding region in Transterm, including codon and GC bias, are available. For each species in Transterm, the initiation and termination regions are aligned by their start or stop codons and presented as base frequency matrices and tables of the information content of the bases in the alignments. Users can obtain summaries of characteristics of the mRNAs for species of their choice and search for translational signals both in the Transterm database and in their own sequence. The current release contains data from over 10 000 species, including the complete genomes of 20 prokaryotes and three eukaryotes. Both flat-file and relational database forms of Transterm are accessible via the WWW at http://biochem.otago.ac.nz/Transterm/     

Mesenchymal-epithelial conversions induced by 5-Azacytidine: Appearance of cytokeratin Endo-A messenger RNA

When mouse-teratocarcinoma-derived fibroblasts (1246 cell line) are subjected to treatment with the inhibitor of DNA methylation, 5-Azacytidine (5 AzaC), they transiently express at 55-kilodalton intermediate-filament protein recognized by the epithelial-specific monoclonal antibody, TROMA-1, although they retain a fibroblastic morphology. However, rare clones (e.g., the 1339 cell line) that permanently express the antigen recognized by TROMA-1 can be derived from the 5 AzaC-treated 1246 population, and these clones have an epithelial phenotype. In the present study, we used cloned DNA probes to demonstrate that, in 1246 fibroblasts, 5 AzaC induces the appearance of Endo-A mRNA. High levels of Endo-A mRNA were also detected in the epithelial derivative, cell line 1339. In both cases, the capping site of the Endo-A mRNA was found to be the same as that in epithelial cells which normally express this RNA.     

Solvent isotope effects on microtubule polymerization and depolymerization

The initial velocity of polymerization of purified beef brain tubulin has been determined at various values of pH or pD in water and in H₂O-D₂O mixtures. D₂O was shown to inhibit both polymerization at 37 °C and depolymerization measured at 5 °C and 37 °C. The microtubules formed in D₂O were indistinguishable from those formed in H₂O, by electron microscope examination. In 93% D₂O the pL²versus rate of polymerization curve was displaced about one unit towards higher pL values. In certain regions of the pL versus rate curve, a stimulation in the rate of polymerization by D₂O is observed. The extent of polymerization at the optimum pL value was not affected by D₂O.     

Structural heterogeneity of human thyroglobulin in relation to its messenger RNA maturation

One human thyroglobulin cDNA clone present 192 nucleotides deletion which correspond to 64 amino-acid deletion on the protein molecule. We show that this fact figure the exon loss on the mRNA molecule using as template during cDNA synthesis by comparison between mRNA and genomic DNA nucleotide sequences. Different possibility can explain this fact. We retain mainly mistake in mRNA maturation fidelity. This type of event is not an exception and can be an explanation for some pathologies.     

Phase-dependent polymerization and depolymerization of actin in Physarum polycephalum nuclei

G- and F-actin contents in physarum polycephalum nuclei isolated during the progress of cell cycle were estimated and compared both by the inhibiting activity of deoxyribonuclease I (DNase I) and by the fractionation on DEAE-Toyopearl column chromatography. The inhibition of DNase appeared maximal in late S phase or early G2 phase and decreased to a minimal value in late G2 phase or M phase, while total actin content in a nucleus, which was analyzed by SDS-polyacrylamide gel electrophoresis as well as by DNase inhibition assay in the presence of 0.75 M guanidine-HCl, did not show such phase-dependent dynamics through the cell cycle.     

Laminin affects polymerization,depolymerization and neurotoxicity of Abeta peptide

Amyloid deposition in Alzheimer fibrils forms neurotoxic senile plaques in a process that may be modulated by associated proteins. In this work we demonstrate the ability of laminin-1 and laminin-2 to inhibit fibril formation and toxicity on cultured rat hippocampal neurons. We confirm that the laminin-1-derived peptide YFQRYLI inhibits efficiently both fibril formation and neurotoxicity and show that the IKVAV peptide inhibits amyloid neurotoxicity despite its slight inhibition of fibril formation. On other hand, laminin-1 induces disaggregation of preformed fibrils in vitro, characterized as a progressive disassembly of fibrils into protofibrils and further clearance of these latter species, leading to a continual inhibition of amyloid neurotoxicity.     

The rates of polymerization and depolymerization of sickle cell hemoglobin

The polymerization and depolymerization of concentrated solutions of sickle cell deoxyhemoglobin were initiated by raising and lowering the temperature, and the time courses of the reactions monitored by the change in apparent turbidity. The polymerization reaction exhibits a marked lag phase followed by a rapid increase in turbidity, and is dependent on a very high power of the hemoglobin concentration, roughly the fifteenth. The depolymerization reaction exhibits no such lag, and is much less dependent on concentration. The implications of these results for polymerization models are discussed.     

RNA of RNA Tumour Viruses contains Poly A

Molecular hybridization with radioactive polyuridylic acid has been used to detect regions of polyadenylic acid in virus RNA. On the average, RNA from tumour viruses is twenty-five to fifty-fold richer in polyadenylic acid than RNA from non-oncogenic viruses. Polyacrylamide gel electrophoresis permitted a qualitative distinction between RNA preparations from the two virus classes.     

Actin depolymerization and polymerization are required during apoptosis in endothelial cells

In order to understand the role of actin microfilaments in the apoptotic process, we followed their evolution during tumor necrosis factor-alpha (TNF)-induced apoptosis in bovine aortic endothelial (BAE) cells. Using Western blotting analysis and immunofluorescence microscopy, we observed that the actin microfilaments network was disrupted in apoptotic cells. Depolymerization of F-actin was concomitant with internucleosomal DNA degradation and with the morphological changes associated with apoptotic cell death. However, using the actin microfilament disrupting agent, cytochalasin, we present evidence that the formation of blebs leading to apoptotic cell fragmentation requires neopolymerization of actin. Indeed, in the presence of cyochalasin, induction of apoptosis (internucleosomal DNA degradation) in BAE cells by TNF and cycloheximide was not associated with these classical morphological markers of apoptosis. Moreover, when added to BAE cells showing incipient apoptotic fragmentation, cytochalasin E reversed this process. We also observed an accumulation of actin at the basis of the apoptotic bodies in formation in these cells. Together, these results suggest that the actin network of flattened cells is disrupted concomitantly to the morphological modifications associated to the apoptotic cell death, and that the cytochalasin-sensitive reorganisation of actin is required to the formation of apoptotic blebs.     

Translation and messenger RNA secondary structure

The possibility of translation being influenced by the messenger RNA secondary structure is investigated with the aid of a stochastic model. Simulations indicate that, at least for certain mRNA's, the mean ribosomal passage time decreases as the mean number of ribosomes on the messenger is increased. Furthermore, large variations in the passage times are found, in accordance with recent experimental results.     

Structural and functional characterization of human telomerase RNA processing and cajal body localization signals

The RNA component of human telomerase (hTR) includes H/ACA and CR7 domains required for 3' end processing, localization, and accumulation. The terminal loop of the CR7 domain contains the CAB box (ugAG) required for targeting of scaRNAs to Cajal bodies (CB) and an uncharacterized sequence required for accumulation and processing. To dissect out the contributions of the CR7 stem loop to hTR processing and localization, we solved the solution structures of the 3' terminal stem loops of hTR CR7 and U64 H/ACA snoRNA, and the 5' terminal stem loop of U85 C/D-H/ACA scaRNA. These structures, together with analysis of localization, processing, and accumulation of hTRs containing nucleotide substitutions in the CR7 domain, identified the sequence and structural requirements of the hTR processing and CB localization signals and showed that these signals are functionally independent. Further, 3' end processing was found to be a prerequisite for translocation of hTR to CBs.     

Defining mechanisms of actin polymerization and depolymerization during dendritic spine morphogenesis

Dendritic spines are small protrusions along dendrites where the postsynaptic components of most excitatory synapses reside in the mature brain. Morphological changes in these actin-rich structures are associated with learning and memory formation. Despite the pivotal role of the actin cytoskeleton in spine morphogenesis, little is known about the mechanisms regulating actin filament polymerization and depolymerization in dendritic spines. We show that the filopodia-like precursors of dendritic spines elongate through actin polymerization at both the filopodia tip and root. The small GTPase Rif and its effector mDia2 formin play a central role in regulating actin dynamics during filopodia elongation. Actin filament nucleation through the Arp2/3 complex subsequently promotes spine head expansion, and ADF/cofilin-induced actin filament disassembly is required to maintain proper spine length and morphology. Finally, we show that perturbation of these key steps in actin dynamics results in altered synaptic transmission.