Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family

A variety of RNA methyltransferases act during ribosomal RNA maturation to modify nucleotides in a site-specific manner. However, of the 10 base-methylated nucleotides present in the small ribosomal subunit of Escherichia coli, only three enzymes responsible for modification of four bases are known. Here, we show that the protein encoded by yggJ, a member of the uncharacterized DUF558 protein family of predicted alpha/beta (trefoil) knot methyltransferases is responsible for methylation at U1498 in 16S rRNA. The gene is well-conserved across bacteria and plants, and likely performs the same function in other organisms. A yggJ deletion strain lacks the methyl group at U1498 as well as the specific methyltransferase activity. Moreover, purified recombinant YggJ specifically methylates m3U1498 in vitro. The deletion strain was unaffected in exponential growth in rich or minimal media at multiple temperatures, but it was defective when grown in competition with isogenic wild-type cells. Based on these data, we conclude that yggJ is the founding member of a family of RNA base methyltransferases, and propose that it be renamed rsmE.     

‘3H-testosterone distribution and binding in RAT thymus cells in vivo’

Summary Autoradiography and biochemical investigations showed that [³H]-testosterone where injected intraperitoneally into male white rats was incorporated rapidly into thymus lymphocytes. Thymic cortex contained more silver grains than medulla, and larger lymphocytes were more labelled than medium or small lymphocytes.Cytosol fraction of thymus cells labelledin vivo with [³H]-testosterone, contained the largest quantity of labelled hormone. A 4S cytosol fraction binds [³H]-testosterone. This could be separated by Sephadex chromatography or by linear sucrose gradient centrifugation. Nuclear extract contained also a small quantity of the labelled hormone.     

DafA cycles between the DnaK chaperone system and translational machinery

DafA is encoded by the dnaK operon of Thermus thermophilus and mediates the formation of a highly stable complex between the chaperone DnaK and its co-chaperone DnaJ under normal growth conditions. DafA(Tth) contains 87 amino acid residues and is the only member of the DnaK(Tth) chaperone system for which no corresponding protein has yet been identified in other organisms and whose particular function has remained elusive. Here, we show directly that the DnaK(Tth)-DnaJ(Tth)-DafA(Tth) complex cannot represent the active chaperone species since DafA(Tth) inhibits renaturation of firefly luciferase by suppressing substrate association. Since DafA(Tth) must be released before the substrate proteins can bind we hypothesized that free DafA(Tth) might have regulatory functions connected to the heat shock response. Here, we present evidence that supports this hypothesis. We identified the 70S ribosome as binding target of free DafA(Tth). Our results show that the association of DafA(Tth) and 70S ribosomes does not require the participation of DnaK(Tth) or DnaJ(Tth). On the contrary, the assembly of DnaK(Tth)-DnaJ(Tth)-DafA(Tth) and ribosome-DafA(Tth) complexes seems to be competitive. These findings strongly suggest the involvement of DafA(Tth) in regulatory processes occurring at a translational level, which could represent a new mechanism of heat shock response as an adaptation to elevated temperature.     

Degradation of ribosomal RNA during starvation: comparison to quality control during steady-state growth and a role for RNase PH

Ribosomal RNAs are generally stable in growing Escherichia coli cells. However, their degradation increases dramatically under conditions that lead to slow cell growth. In addition, incomplete RNA molecules and molecules with defects in processing, folding, or assembly are also eliminated in growing cells in a process termed quality control. Here, we show that there are significant differences between the pathways of ribosomal RNA degradation during glucose starvation and quality control during steady-state growth. In both processes, endonucleolytic cleavage of rRNA in ribosome subunits is an early step, resulting in accumulation of large rRNA fragments when the processive exoribonucleases, RNase II, RNase R, and PNPase are absent. For 23S rRNA, cleavage is in the region of helix 71, but the exact position can differ in the two degradative processes. For 16S rRNA, degradation during starvation begins with shortening of its 3' end in a reaction catalyzed by RNase PH. In the absence of this RNase, there is no 3' end trimming of 16S rRNA and no accumulation of rRNA fragments, and total RNA degradation is greatly reduced. In contrast, the degradation pattern in quality control remains unchanged when RNase PH is absent. During starvation, the exoribonucleases RNase II and RNase R are important for fragment removal, whereas for quality control, RNase R and PNPase are more important. These data highlight the similarities and differences between rRNA degradation during starvation and quality control during steady-state growth and describe a role for RNase PH in the starvation degradative pathway.     

Responses of the digestive tract of the omnivorous northern brown bandicoot, Isoodon macrourus (Marsupialia: Peramelidae), to plant- and insect-containing diets

The gastrointestinal tract of omnivores such as bandicoots (Marsupialia: Peramelidae) must be able to process foods as different as invertebrates, fungi and plant material. We studied the mechanisms involved in the utilisation by captive northern brown bandicoots (Isoodon macrourus) of insect larvae and milled lucerne (Medicago sativa) hay incorporated into a basal diet of a commercial small carnivore mix. Animals on the plant-basal mix digested less dry matter, energy, lipid, fibre and total nitrogen, but consumed 79% more dry matter than those on the insect-basal mix. Consequently intake of digestible energy (i.e. energy absorbed) was not significantly different between diets. Mean retention time (MRT, the mean time a marker remains in the tract) of a large particle marker was shorter on the plant-basal mix, reflecting its higher intake, but MRT of a solute marker was not significantly different between diets. Consequently the solute marker was retained longer than the particle marker on the plant-basal mix, indicating selective retention of solutes and very small particles in the caecum on this diet. This was confirmed by a higher proportion of small particles in the caecum than the distal colon of road-killed I. macrourus. Thus the main responses by I. macrourus to the plant-basal mix appeared to be an increase in gastrointestinal tract capacity (from radiographic evidence), selective retention of solutes and very small particles in the caecum, and facilitated passage of less tractable large particles through the colon. As a consequence, food intake was higher on the plant-basal mix, which compensated for its lower digestibility, and intake of digestible energy was similar to that on the insect-basal mix. This considerable flexibility of the morphologically rather simple digestive tract of northern brown bandicoots helps to explain their ability to cope with naturally variable diets consisting of mainly invertebrates in summer to much more plant and fungal material in winter, and to survive in nutritionally dynamic environments such as heathlands where there can be dramatic changes in food type and availability following periodic wildfires. Accepted: 14 April 1999     

Substrate recognition by AAA+ ATPases: distinct substrate binding modes in ATP-dependent protease Yme1 of the mitochondrial intermembrane space

The energy-dependent proteolysis of cellular proteins is mediated by conserved proteolytic AAA(+) complexes. Two such machines, the m- and i-AAA proteases, are present in the mitochondrial inner membrane. They exert chaperone-like properties and specifically degrade nonnative membrane proteins. However, molecular mechanisms of substrate engagement by AAA proteases remained elusive. Here, we define initial steps of substrate recognition and identify two distinct substrate binding sites in the i-AAA protease subunit Yme1. Misfolded polypeptides are recognized by conserved helices in proteolytic and AAA domains. Structural modeling reveals a lattice-like arrangement of these helices at the surface of hexameric AAA protease ring complexes. While helices within the AAA domain apparently play a general role for substrate binding, the requirement for binding to surface-exposed helices within the proteolytic domain is determined by the folding and membrane association of substrates. Moreover, an assembly factor of cytochrome c oxidase, Cox20, serves as a substrate-specific cofactor during proteolysis and modulates the initial interaction of nonassembled Cox2 with the protease. Our findings therefore reveal the existence of alternative substrate recognition pathways within AAA proteases and shed new light on molecular mechanisms ensuring the specificity of proteolysis by energy-dependent proteases.     

Yellow nail syndrome: treatment of lymphedema using low pressure compression

The present report describes a case with the triad of yellow nail syndrome (YNS) and the use of low-pressure compression pump as treatment of lymphedema in YNS. A 71-year-old woman presented with bilateral lower extremity lymphedema, yellow nails, and recurrent bilateral pleural effusion. In this case, we specifically focused on lymphedema treatment of the legs besides other recommendations for YNS.     

Amphiphilic and thermosensitive copolymers based on pullulan and Jeffamine: Synthesis, characterization and physicochemical properties

The synthesis of thermosensitive copolymers based on pullulan and polyether amine was performed in water using a water-soluble carbodiimide and N-hydroxysuccinimide as activators. Jeffamine^® M2005 was chosen as a polyether to impart thermosensitive character to the copolymer. Pullulan was modified into carboxymethylpullulan, to bring carboxylate groups to the polysaccharide so as to further the grafting reaction. The copolymers were characterized by FT-IR, ¹H NMR spectroscopy and molecular weights measurements (by SEC coupled with MALS/DRI/Viscometer lines). The thermosensitive behaviour of CMP-g-M2005 copolymers was studied by fluorescence spectroscopy of pyrene, by rheometry and microDSC measurements. The sol-gel transition temperature was found dependent on the solvent, the grafting degree of M2005 and the concentration of the copolymer. For example it was 35 °C in water, 28 °C in acid buffer (0.1 M, pH 5.4) and 26 °C in saline phosphate buffer (0.15 M, pH 7.4) for a grafting degree of 0.20 at a concentration of 5 wt%.     

Critical steps in tissue processing in histopathology

Histopathological diagnosis using Formalin-Fixed Paraffin Embedded (FFPE) tissues is essential for the prognostic and therapeutic management of cancer patients. Pathologists are being confronted with increasing demands, from both clinicians and patients, to provide immunophenotypic and gene expression data from FFPE tissues to allow the planning of personalized therapeutic regimens. Recent improvements in the protocols for pre-analysis processing of pathological tissues aim to better preserve cellular details and to conserve antigens and nucleic acid sequences. These developments have been recently patented. The international protocol for the transporting of surgical specimens from the surgical theatre to the pathology department is to immerse the specimen in formalin. The alternative method of sealing the specimens into bags under a vacuum and then cooling is a well-accepted and environmentally safe procedure that overcomes the many drawbacks linked to transfer in formalin. Importantly, RNA is notoriously poorly preserved in FFPE tissue. Due to this, successful procedures for the extraction of genetic information from archival tissues have been the object of several studies and patents. Novel molecular approaches for RT-qPCR and gene array analysis on FFPE tissues are presented here. Moreover, a major advance is reported in this study, the observation that tissue fixation in cold conditions allows a much better preservation of nucleic acid sequences.