Different modes of interaction by TIAR and HuR with target RNA and DNA

TIAR and HuR are mRNA-binding proteins that play important roles in the regulation of translation. They both possess three RNA recognition motifs (RRMs) and bind to AU-rich elements (AREs), with seemingly overlapping specificity. Here we show using SPR that TIAR and HuR bind to both U-rich and AU-rich RNA in the nanomolar range, with higher overall affinity for U-rich RNA. However, the higher affinity for U-rich sequences is mainly due to faster association with U-rich RNA, which we propose is a reflection of the higher probability of association. Differences between TIAR and HuR are observed in their modes of binding to RNA. TIAR is able to bind deoxy-oligonucleotides with nanomolar affinity, whereas HuR affinity is reduced to a micromolar level. Studies with U-rich DNA reveal that TIAR binding depends less on the 2'-hydroxyl group of RNA than HuR binding. Finally we show that SAXS data, recorded for the first two domains of TIAR in complex with RNA, are more consistent with a flexible, elongated shape and not the compact shape that the first two domains of Hu proteins adopt upon binding to RNA. We thus propose that these triple-RRM proteins, which compete for the same binding sites in cells, interact with their targets in fundamentally different ways.     

Cholera toxin and thyrotropine can replace natural inducers required for the metamorphosis of larvae and buds of the scyphozoanCassiopea andromeda

Summary The scyphozoan medusaCassiopea andromeda forms free swimming planulae and buds that metamorphose into tentacle bearing sedentary polyps. About 30% of the planulae and 7% of the buds undergo such metamorphosis within 30 days in sterile natural seawater from the Red Sea. In sterile artificial sea water devoid of any organic substances, normal metamorphosis does not take place. This indicates that both the planulae and the buds require organic morphogenetic inducers present in the sea to settle and metamorphose. The addition of cholera toxin or thyrotropin to preparations of sterile artificial sea water, induced normal metamorphosis. These inducers enhanced the rate of metamorphosis and up to 100% of the planulae and buds formed polyps within 2–18 days. We conclude that our preparations of cholera toxin and thyrotropin mimic the action of natural inducers.     

Glia Modulate a Neuronal Circuit for Locomotion Suppression during Sleep in C. elegans

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First record of the Brassy Chub Kyphosus vaigiensis (Quoy & Gaimard, 1825) in the Eastern Mediterranean (Osteichthyes: Perciformes: Kyphosidae)

The Brassy Chub, Kyphosus vaigiensis, first recorded in the Mediterranean in 1998, is reported herein from the coast of Israel. The identity of the specimen was confirmed by morphological and molecular analysis. This is the first record of K. vaigiensis from the Eastern Mediterranean. The possible origins of the Israeli record is discussed.     

The effect of membrane potential on the redox state of cytochromeb 561 in antimycin-inhibited submitochondrial particles

The oxidation of cytochromeb ₅₆₁ by ATP was measured in submitochondrial particles inhibited by antimycin. The redox potential of the bulk (M phase) was controlled by the ratio of fumarate:succinate, and the oxidation of cytochromeb was calculated and expressed as a change in redox potential (E _h) measured in millivolts. The oxidation of cytochromeb ₅₆₁ is an energy-driven reaction affected only by the component of the proton motive force. The oxidation (measured in millivolts) is a function of the phosphate potential, reaching a maximal value of 40 mV at G_ATP<–12 kcal/mole. The maximal measured value of ATP-dependent was 100 mV. Thus only a fraction of the membrane potential effects the redox state of cytochromeb ₅₆₁. In contrast to the ATP-induced oxidation of cytochromeb ₅₆₁, cytochromeb ₅₆₆ is in redox equilibrium with fumarate succinate either in the presence or in the absence of ATP. The selective oxidation ofb ₅₆₁ is explained within the term of theQ cycle as a reflection of on the electron electrochemical potential. The positive electric potential of theC phase causes cytochromeb ₅₆₆ to act as oxidant with respect to cytochromeb ₅₆₁. In the presence of antimycin cytochromeb ₅₆₁ cannot equilibrate with the quinone and undergoes oxidation, while cytochromeb ₅₆₆ reequilibrates with the quinone and thus regains redox equilibrium with the fumarate succinate redox buffer.Abbreviations used: ETP_H, phosphorylating submitochondrial particles; TMPD,N ₁ N ₁ NN-tetramethyl-p-phenylenediamine; FCCP, carbonylcyanidep-trifluoromethoxyphenylhydrazone; Mes, 2-(N-morpholino) ethanesulfonic acid.     

Human leukocyte interferon: Isolation and characterization of several molecular forms

Purification of human leukocyte interferon by high-performance liquid chromatography yielded eight major interferon species. These were characterized by their molecular weight, amino acid composition, and antiviral activity on human and bovine cells. The molecular weights of the purified species ranged from 16,000 to 21,000. The tryptic peptide profiles of all the pure species were compared. Both amino acid compositions and tryptic peptide profiles revealed a structural similarity among the various species.     

Isolation and assessment of phytate-hydrolysing bacteria from the DelMarVa Peninsula

The Delaware-Maryland-Virginia (DelMarVa) Peninsula, flanking one side of the Chesapeake Bay, is home to a substantial broiler chicken industry. As such, it produces a significant amount of manure that is typically composted and spread onto local croplands as a fertilizer. Phytate (myo inositol hexakisphosphate), the major form of organic phosphorus in the manure, can be hydrolysed by microorganisms to produce orthophosphate. Orthophosphate is a eutrophication agent which can lead to algal blooms, hypoxia and fish kills in the Chesapeake Bay and its tributaries. This transect study reveals a subpopulation of heterotrophic, thiosulfate-utilizing bacteria that can degrade phytate within the watershed as well as its receiving water sediment. Aerobic isolates were typical soil bacteria, e.g. Pseudomonad, Bacillus and Arthrobacter species, as well as a less common Staphylococcus inhabitant. Bacillus pumilus, Staphyloccocus equorum, Arthrobacter bergei and Pseudomonas marginalis strains have not been previously described as phytate-degrading. Each site along the transect - from manure pile to receiving sediment - was host to a population of bacteria that can degrade phytate and hence, each is a possible non-point source of orthophosphate pollution. Each new isolate could provide an enzyme additive for monogastric feed, thus reducing the impact of excessive phytate load on the environment.     

Signal peptide of FadA adhesin from Fusobacterium nucleatum plays a novel structural role by modulating the filament's length and width

FadA, a novel adhesin of periodontal pathogen Fusobacterium nucleatum is composed of two forms, pre-FadA and mature FadA (mFadA), constituting the functional FadA complex (FadAc). By electron microscopy, we observed that mFadA formed uniformly long and thin filaments, while FadAc formed heterogeneous filaments of varying lengths and widths, as well as "knots". Mutants in signal peptide or in the non-alpha-helical loop retaining heterogeneous structures had binding activity while those forming aggregates or long filaments lost activity. These observations suggest short filaments and knots may be the active forms of FadA. This is the first demonstration that a signal peptide is required for the assembly of a bacterial adhesin.     

The mechanism of proton transfer between adjacent sites on the molecular surface

The surface of a protein, or a membrane, is spotted with a multitude of proton binding sites, some of which are only few Å apart. When a proton is released from one site, it propagates through the water by a random walk under the bias of the local electrostatic potential determined by the distribution of the charges on the protein. Eventually, the released protons are dispersed in the bulk, but during the first few nanoseconds after the dissociation, the protons can be trapped by encounter with nearby acceptor sites. While the study of this reaction on the surface of a protein suffers from experimental and theoretical difficulties, it can be investigated with simple model compounds like derivatives of fluorescein. In the present study, we evaluate the mechanism of proton transfer reactions that proceed, preferentially, inside the Coulomb cage of the dye molecules. Kinetic analysis of the measured dynamics reveals the role of the dimension of the Coulomb cage on the efficiency of the reaction and how the ordering of the water molecules by the dye affects the kinetic isotope effect.     

The mechanism of proton transfer between adjacent sites on the molecular surface

The surface of a protein, or a membrane, is spotted with a multitude of proton binding sites, some of which are only few A apart. When a proton is released from one site, it propagates through the water by a random walk under the bias of the local electrostatic potential determined by the distribution of the charges on the protein. Eventually, the released protons are dispersed in the bulk, but during the first few nanoseconds after the dissociation, the protons can be trapped by encounter with nearby acceptor sites. While the study of this reaction on the surface of a protein suffers from experimental and theoretical difficulties, it can be investigated with simple model compounds like derivatives of fluorescein. In the present study, we evaluate the mechanism of proton transfer reactions that proceed, preferentially, inside the Coulomb cage of the dye molecules. Kinetic analysis of the measured dynamics reveals the role of the dimension of the Coulomb cage on the efficiency of the reaction and how the ordering of the water molecules by the dye affects the kinetic isotope effect.