On peptide bond formation, translocation, nascent protein progression and the regulatory properties of ribosomes. Derived on 20 October 2002 at the 28th FEBS Meeting in Istanbul.

High-resolution crystal structures of large ribosomal subunits from Deinococcus radiodurans complexed with tRNA-mimics indicate that precise substrate positioning, mandatory for efficient protein biosynthesis with no further conformational rearrangements, is governed by remote interactions of the tRNA helical features. Based on the peptidyl transferase center (PTC) architecture, on the placement of tRNA mimics, and on the existence of a two-fold related region consisting of about 180 nucleotides of the 23S RNA, we proposed a unified mechanism integrating peptide bond formation, A-to-P site translocation, and the entrance of the nascent protein into its exit tunnel. This mechanism implies sovereign, albeit correlated, motions of the tRNA termini and includes a spiral rotation of the A-site tRNA-3' end around a local two-fold rotation axis, identified within the PTC. PTC features, ensuring the precise orientation required for the A-site nucleophilic attack on the P-site carbonyl-carbon, guide these motions. Solvent mediated hydrogen transfer appears to facilitate peptide bond formation in conjunction with the spiral rotation. The detection of similar two-fold symmetry-related regions in all known structures of the large ribosomal subunit, indicate the universality of this mechanism, and emphasizes the significance of the ribosomal template for the precise alignment of the substrates as well as for accurate and efficient translocation. The symmetry-related region may also be involved in regulatory tasks, such as signal transmission between the ribosomal features facilitating the entrance and the release of the tRNA molecules. The protein exit tunnel is an additional feature that has a role in cellular regulation. We showed by crystallographic methods that this tunnel is capable of undergoing conformational oscillations and correlated the tunnel mobility with sequence discrimination, gating and intracellular regulation.     

Intraspecific Variation in Chemical Attraction of Rice to Insect Predators

The olfactory response of predators of the brown planthopper,Nilaparvata lugensStål, to different genotypes of rice (14 cultivars and breeding lines ofOryza sativaL. and 1 wild species,Oryza nivaraSharma et Shastry) was measured in an airflow olfactometer. Odor from rice plants attracted more females of the mirid predatorCyrtorhinus lividipennisReuter than plain air (control) on only 6 of the 15 rice genotypes. Orientation ofC. lividipennistoward volatiles of certain rice genotypes was apparent even when the plants were free of the brown planthopper. However, the predator distinguished between prey-infested and uninfested plants and preferred plants with eggs over plants with nymphs. The predator did not distinguish different stages of plant growth (vegetative, booting, or flowering). Plants artificially injured to simulate brown planthopper oviposition wounds were not as attractive to the predator as plants on which the planthopper had oviposited. The preassay preconditioning on the cultivar TN1 did not produce a predator bias for this genotype. This suggests that rearing effects or chemically mediated associative learning reported for some natural enemies did not influenceC. lividipennis'host response. Results with another predator, the coccinellidMicraspis hirashimaiSasaji, produced less consistent behavior. Planthopper-infested plants attracted more females ofM. hirashimaithan unifested plants in only 1 of the 12 rice genotypes evaluated. Implications for augmenting predators by rice cultivar selection and modification are discussed.     

Patchiness and disturbance: plant community responses to porcupine diggings in the central Negev

We tested the hypothesis that diversity and productivity of herbaceous plant communities in disturbed soil are related to the physical and biological heterogeneity of the landscape Our study was earned out on vegetation responses in porcupine diggings on a rocky slope in the central Negev desert in Israel We measured aboveground bio-mass and plant density per species in 150 porcupine diggings (15 cm deep and 15 to 20 cm wide) and in equally sized adjacent control samples in the undisturbed soil matrix We calculated mean annual biomass production, plant density and species richness for 10 sample areas along the slope In addition, we divided the plants into groups according to propagule size and dispersal mode We denoted two types of landscape heterogeneity, which we called physical and biological patchiness Physical patchiness was measured as the ratio of bare rock to soil surface Biological patchiness was the area of the soil covered by shrubs with associated soil mound and under-story relative to the total soil surface We also measured disturbance density, as the long term (17 yr) average density of newly made porcupine diggings We found that 1) the physical patchiness explained 30% of the variation of biological patchiness along the slope, while 2) the patterns of disturbance intensity and biological patchiness were similar (R-=0 386) 3) Biomass, density and species richness were significantly higher in diggings than m the soil matrix 4) Plant density in the matrix, but not m the diggings, was significantly correlated with physical patchiness, 5) species richness in diggings was significantly correlated with biological patchiness, but 6) biomass production in diggings and matrix was not affected by either physical or biological patchiness of the landscape 7) Disturbance density did not affect vegetation responses in diggings and matrix 8) A shift in the plant communities in the matrix towards plants with smaller seeds was associated with increasing physical patchiness, while m diggings there was an opposite shift 9) The proportion of wind dispersers was higher in diggings than outside, while the proportion of runoff dispersers was lower, 10) the densities of runoff dispersers in diggings and matrix were positively correlated with physical and biological patchiness 11) Physical and biological patchiness formed the two major gradients of species composition, explaining 30 and 25% respectively We conclude that the network of physical and biological patchiness and soil disturbance are important in the redistribution of resources and seeds, which control plant biomass, density, species richness and diversity The bare rock surface is the main source for runoff flow with associated soil, organic matter and nutrients The understory vegetation of shrubs provides seeds for creating and maintaining diversity The soil matrix absorbs runoff flow, and disturbances absorb runoff and trap seeds Thus, differences in landscape heterogeneity and their effects on resource and seed movement interact in controlling plant community productivity and diversity in the landscape     

Lack of effect of toxic aluminium concentrations on nitrogen fixation by nodulatedStylosanthes species

Summary Effects of three solution aluminium concentrations (0, 25, and 100M) on nitrogen fixation by well-nodulated plants ofStylosanthes hamata, Stylosanthes humilis andStylosanthes scabra are reported. Plants were inoculated with Rhizobium CB756 and grown for 21 days in an aluminium-free nutrient solution at pH 5.3 before imposition of the aluminium treatments.Nitrogen fixation was measured both by the increase in total nitrogen content of the plants and acetylene reduction in roots of plants harvested at 10 and 20 days after imposition of the aluminium treatments. Solution aluminium concentrations as high as 100M, had no detrimental effect on nitrogen fixation in any species.     

35Cl nuclear magnetic resonance studies of anion binding to halophilic proteins: Ferredoxin from Halobacterium of the Dead Sea

The anion-binding characteristics of ferredoxin from Halobacterium of the Dead Sea have been studied by ³⁵Cl^? NMR. It is found that the binding constant of Cl^? to halophilic ferredoxin is ca. 0.09 at 28 °C and that the binding enthalpy is positive. It is also found that the correlation time for chloride ions bound to halophilic ferredoxin is about 10 ns. The effect on the ³⁵Cl^?1 NMR signal of adding competing anions is also studied. Halophilic proteins like ferredoxin which have a high negative charge bind anions with low affinity but the ³⁵Cl^? quadrupole relaxation technique can conveniently monitor such weak binding.     

Inhibition of the predatory activity ofBdellovibrio by various environmental pollutants

The predatory activity of bdellovibrios is affected by various environmental pollutants such as detergents, heavy metals, and pesticides. This was shown in a two-membered system ofBdellovibrio andPhotobacterium, in which the effect of the predator on the bioluminescence of the prey indicated the activity of the former. The high sensitivity of the bdellovibrios toward certain chemicals (e.g., CdCl₂) indicates the possibility of using the system for biological monitoring of those chemicals.     

Bacteriorhodopsin in a bloom of halobacteria in the Dead Sea

A dense bloom of red halobacteria developed in the Dead Sea in the summer 1980, bacterial densities of up to 1.9 x10⁷ cells ml^-1 were observed. The population consisted of two types: pleomorphic, cup-shaped cells and rod-shaped cells. A high content of bacteriorhodopsin was found in the bloom (up to 0.4 nmol per mg protein). The rod-shaped Halobacterium was isolated and was shown to contain bacteriorhodopsin.Abbreviations 20 specific gravity at 20°C - Tris Tris-(hydroxymethyl)-aminomethane     

Effects of temperature and molecular interactions on the vibrational infrared spectra of phospholipid vesicles

Infrared spectra were obtained as a function of temperature for a variety of phospholipid/water bilayer assemblies (80% water by weight) in the 3000-950 cm^?1 region. Spectral band-maximum frequency parameters were defined for the 2900 cm^?1 hydrocarbon chain methylene symmetric and asymmetric stretching vibrations. Temperature shifts for these band-maximum frequencies provided convenient probes for monitoring the phase transition behavior of both multilamellar liposomes and small diameter single-shell vesiclesof dipalmitoyl phosphatidylcholine/water dispersions. As examples of the effects of bilayer lipid/cholesterol/water (3 : 1 mol ratio) and lipid/cholesterol/amphotericin B/water (3 : 1 : 0.1 mol ratios) vesicles were examined using the methylene stretching frequency indices. In comparison to the pure vesicle form, the transition width of the lipid/cholesterol system increased by nearly a factor of two (to 8°C) while the phase transition temperature remained approximately the same (41° C). For the lipid/cholesterol/amphotericin B system, the phase transition temperature increased by about 4.5° C (to 45.5°C) with the transition width increasing by nearly a factor of four ($\text{to}\text{≈ 15°}\text{C}$) above that of the pure vesicles. The lipid/cholesterol/amphotericin B data were interpreted as reflecting the formation below 38°C of a cholesterol/amphotericin B complex whose dissociation at higher temperature (38–60°C range) significantly broades the gel-liquid crystalline phase transition.