The C. elegans Polycomb gene SOP-2 encodes an RNA binding protein

Epigenetic silencing of Hox cluster genes by Polycomb group (PcG) proteins is thought to involve the formation of a stably inherited repressive chromatin structure. Here we show that the C. elegans-specific PcG protein SOP-2 directly binds to RNA through three nonoverlapping regions, each of which is essential for its localization to characteristic nuclear bodies and for its in vivo function in the repression of Hox genes. Functional studies indicate that the RNA involved in SOP-2 binding is distinct from either siRNA or microRNA. Remarkably, the vertebrate PcG protein Rae28, which is functionally and structurally related to SOP-2, also binds to RNA through an FCS finger domain. Substitution of the Rae28 FCS finger for the essential RNA binding region of SOP-2 partially restores localization to nuclear bodies. These observations suggest that direct binding to RNA is an evolutionarily conserved and potentially important property of PcG proteins.     

Cytosolic delivery of macromolecules. 3. Synthesis and characterization of acid-sensitive bis-detergents

A serious limitation that precludes utilization of single-tailed, pH-sensitive detergents for the cytosolic delivery of macromolecules is their low limit of incorporation in stable liposomal formulations. To address this issue, we have prepared two Gemini surfactants or 'bis-detergents' by cross-linking the headgroups of single-tailed, tertiary amine detergents through oxyethylene (BD1) or acid-labile acetal (BD2) moieties. The membrane-bound pK(a) of the twin tertiary amine headgroups was determined to be 6.37 +/- 0.36 using a fluorescence-based assay. As evidenced by thin-layer chromatography, BD2was hydrolyzed under acidic conditions (pH 5.0) with an approximate half-life of 3 h at 37 degrees C, while BD1 remained stable. Low pH-induced collapse of liposomes containing acid-labile BD2 into micelles was more facile than that of BD1. With BD1, the process appeared to be reversible in that aggregation of micelles was observed at basic pH. The irreversible lamellar-to-micellar transition observed with BD2-containing liposomes can possibly be attributed to acid-catalyzed hydrolysis of the acetal cross-linker, which generates two detergent monomers within the bilayer. Liposomes composed of 75 mol % bis-detergent and 25 mol % phosphatidylcholine were readily prepared and could entrap macromolecules such as polyanionic dextran of MW 40 kDa with moderate efficiency. The ability of BD2-containing liposomes to promote efficient cytosolic delivery of antisense oligonucleotides was confirmed by (a) their diffuse intracellular distribution seen in fluorescence micrographs, and (b) the up-regulation of luciferase in an antisense functional assay. The low pH-responsive, bis-detergent constructs described herein are suitable for triggered release strategies targeted to acidic intracellular or interstitial environments.     

Differences in evolutionary pressure acting within highly conserved ortholog groups

Background  

In highly conserved widely distributed ortholog groups, the main evolutionary force is assumed to be purifying selection that enforces sequence conservation, with most divergence occurring by accumulation of neutral substitutions. Using a set of ortholog groups from prokaryotes, with a single representative in each studied organism, we asked the question if this evolutionary pressure is acting similarly on different subgroups of orthologs defined as major lineages (e.g. Proteobacteria or Firmicutes).     

Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences

Background  

Computational predictions are critical for directing the experimental study of protein functions. Therefore it is paradoxical when an apparently erroneous computational prediction seems to be supported by experiment.     

Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold

Background  

The β-grasp fold (β-GF), prototyped by ubiquitin (UB), has been recruited for a strikingly diverse range of biochemical functions. These functions include providing a scaffold for different enzymatic active sites (e.g. NUDIX phosphohydrolases) and iron-sulfur clusters, RNA-soluble-ligand and co-factor-binding, sulfur transfer, adaptor functions in signaling, assembly of macromolecular complexes and post-translational protein modification. To understand the basis for the functional versatility of this small fold we undertook a comprehensive sequence-structure analysis of the fold and developed a natural classification for its members.     

Pebrine diagnosis using quantitative phase imaging and machine learning

Pebrine is the most dreaded infectious disease of the silkworm and has devastated sericulture in Europe during the 18th century. Thereafter, if it is detected, the crop is burned to prevent further dissemination. The conventional microscopic examination of moth's body fluid is erroneous and it exacerbates on Metarhizium anisopliae (MA) contaminated test samples. This is due to the resemblance of pebrine and MA spores in the microscopic examination. Therefore, this study aims to demonstrate an efficient pebrine detection technique. In the proposed method, a motorised brightfield microscope is custom-made to acquire focused and defocused images of test spores. These images are used to produce quantitative phase images of the spores by the transport of intensity equation method. The phase images' histogram of oriented gradients feature is used by a machine learning classifier to categorise the spores. This system classified 92 pebrine and 185 MA spores with an accuracy of 97% at 0.04 seconds/spore. The duration taken for image acquisition is 2.5 minutes per sample (10 fields of view covering an area of 302 × 260 μm²). The proposed method shows reliable results in pebrine diagnosis and would be an efficient alternative for current approaches.     

GSH Transport in Immortalized Mouse Brain Endothelial Cells

We have previously shown GSH transport across the blood-brain barrier in vivo and expression of transport in Xenopus laevis oocytes injected with bovine brain capillary mRNA. In the present study, we have used MBEC-4, an immortalized mouse brain endothelial cell line, to establish the presence of Na+-dependent and Na+-independent GSH transport and have localized the Na+-dependent transporter using domain-enriched plasma membrane vesicles. In cells depleted of GSH with buthionine sulfoximine, a significant increase of intracellular GSH could be demonstrated only in the presence of Na+. Partial but significant Na+ dependency of [35S]GSH uptake was observed for two GSH concentrations in MBEC-4 cells in which gamma-glutamyltranspeptidase and gamma-glutamylcysteine synthetase were inhibited to ensure absence of breakdown and resynthesis of GSH. Uniqueness of Na+-dependent uptake in MBEC-4 cells was confirmed with parallel uptake studies with Cos-7 cells that did not show this activity. Molecular form of uptake was verified as predominantly GSH, and very little conversion of [35S]cysteine to GSH occurred under the same incubation conditions. Poly(A)+ RNA from MBEC expressed GSH uptake with significant (approximately 40-70%) Na+ dependency, whereas uptake expressed by poly(A)+ RNA from HepG2 and Cos-1 cells was Na+ independent. Plasma membrane vesicles from MBEC were separated into three fractions (30, 34, and 38% sucrose, by wt) by density gradient centrifugation. Na+-dependent glucose transport, reported to be localized to the abluminal membrane, was found to be associated with the 38% fraction (abluminal). Na+-dependent GSH transport was present in the 30% fraction, which was identified as the apical (luminal) membrane by localization of P-glycoprotein 170 by western blot analysis. Localization of Na+-dependent GSH transport to the luminal membrane and its ability to drive up intracellular GSH may find application in the delivery of supplemented GSH to the brain in vivo.