2 A prebiotic RNA apparatus functions within the contemporary ribosome

Ribosomes, the universal cellular machines, possess spectacular architecture accompanied by inherent mobility, allowing for their smooth performance as polymerases that translate the genetic code into proteins. The site for peptide bond formation is located within a universal internal semi-symmetrical region, which was identified within all contemporary ribosomes. The high conservation of this region implies its existence irrespective of environmental conditions and indicates that it may represent an ancient RNA molecular apparatus. Hence, we named it the “proto-ribosome”. This prebiotic pocket-like RNA entity is suggested to be capable to accommodate substrates whose stereochemistry enables the creation of chemical bonds. It could have evolved from an earlier catalytic RNA entity that we named the “pre-proto-ribosome”, presumed to be a molecular machine capable of performing various essential tasks in the RNA world, which was snatched by the amino acid invaders for producing proteins.     

Autoradiographic Analysis of [3H]Imipramine Binding in the Human Brain Postmortem: Effects of Age and Alcohol

In vitro quantitative autoradiography of high-affinity [3H]imipramine binding sites was performed on 16 human brains postmortem. The densities of binding sites were highest in the hypothalamus. Next, in descending order, were the basal and lateral nuclei of the amygdala; substantia innominata; insular cortex; the central nucleus of the amygdala; the anterior nucleus of the thalamus; the head of the caudate nucleus; portions of the frontal, parietal, and temporal cortex; claustrum; the granular layer of the dentate gyrus; substantia nigra; the pyramidal layer of CA fields; globus pallidus; red nucleus; and white matter. Imipramine binding was found to increase with age in a region-specific manner. The presence of alcohol had a similar effect, which was most pronounced in the hippocampus. Sex and time from death to autopsy did not affect imipramine binding, in our sample.     

Effect of Chronic Desipramine Treatment on Dihydroalprenolol, Imipramine, and Desipramine Binding Sites: A Quantitative Autoradiographic Study in the Rat Brain

Desmethylimipramine (DMI) administered once daily for 10 days caused a significant decrease in beta-adrenergic receptor binding, as measured by quantitative autoradiography in discrete brain regions. The decrease was observed 72 h after the last injection throughout the cortex and in hippocampus but not in other regions, much richer in beta-receptors, such as the caudate, olfactory tubercle, superior colliculus, dorsomedial thalamus, substantia nigra, or pineal. The same paradigm did not affect imipramine (IMI) binding in the cortex or in regions with high concentrations of IMI binding sites. DMI binding was not decreased, either. Significant increases in DMI binding were observed in frontal cortex and in the ventral aspect of the bed nucleus of the stria terminalis. We conclude that a reduction in tricyclic binding is not a general phenomenon following chronic treatment with tricyclic antidepressants, and changes in binding, when they do occur, are not correlated with areas of high binding site density.     

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.     

Colonization in an abandoned East-Mediterranean vineyard

Abstract. Previous studies on secondary succession in abandoned agricultural land in the Mediterranean area were carried out by the chronosequence method, including data from different sites. A unique opportunity to study secondary succession arose from a situation in which different parts of one homogeneous East-Mediterranean vineyard were abandoned for 5, 8, 15 and 35 yr, and did not suffer from any disturbance subsequently. Most of the perennial species that colonized the abandoned vineyard were fleshy fruited species, which apparently were dispersed by birds from the surrounding maquis into the vineyard. These bird-dispersed species were the first to be established, and were the dominant plant group according to dispersal modes. The abandoned vine plants and their supporting columns provided the birds with perching and feeding sites, enhancing the arrival of bird-dispersed species regardless of their life forms. Under these conditions the most important attribute that affected vegetation dynamics was seed dispersal mode. Trees were among the first to colonize in the vineyard, implying that no facilitation was needed for their establishment. Annual plant species were the only species to disappear during succession. Almost all perennial species which had arrived persisted in the vineyard, and no replacement of perennial species was found. The rate of succession was rapid, as expressed by the short time (8–15 yr) needed for the stabilization of species composition, for growth to average height of late succession trees, and for reaching high cover of the invading perennial species in the abandoned vineyard. The secondary succession described above differs from that in the western Mediterranean by the absence of perennial species replacement and its rapid rate. The possible causes are discussed.     

The maintenance ofBdellovibrio at low prey density

A mathematical model for the interaction ofBdellovibrio and its prey predicted that a relatively high prey density (7×10⁵ cells ml^–1) would be required for the establishment of an equilibrium in a mixed population [8]. The present report shows thatBdellovibrio can be maintained in a continuous culture when the prey cell density is much lower (2–5×10⁴ cells ml^–1), and closer to that of naturally occurring bacterial populations in sea waters.     

Spatial pattern of seedlings 1 year after fire in a Mediterranean pine forest

Summary The spatial distribution of seedlings of the dominant perennial plant species (Pinus halepensis, Cistus salviifolius, Rhus coriaria) and may annual species was studied after a wild fire in an eastern Mediterranean pine forest. The spatial distribution of all seedlings is affected by the location of the old burned pine trees. Seedling density of Pinus and Cistus is higher at a distance from the burned pine canopy and lower near the burned pine trunk. It is also higher beneath small burned pine trees than under big ones. Rhus seedling density is higher under big burned pine trees and also near the burned trunks. Seedlings of Pinus, Cistus and Rhus growing under the burned canopy of big pine trees tend to be taller than seedlings under small ones or outside the burned canopy. Most annual species germinate and establish themselves outside the burned canopies, and only a few annual species are found beneath them. It is suggested that variation in the heat of the fire, in the amount of ash between burned pine trees of different sizes, and in the distance from the burned canopy are responsible for the observed pattern of seedling distribution. The possible ecological significance of the spatial pattern of seedlings distribution and their differential growth rate are discussed.     

A Unique Ascorbate Peroxidase Active Component in the Cyanobacterium Synechococcus PCC 7942 (R2)

Ascorbate peroxidase active component (APAC) was purified and characterized in Synechococcus PCC 9742 (R2) cells. APAC was isolated from freshly harvested cells, by ion exchange chromatography on DEAE cellulose, ultrafiltration through a 3000 dalton cut off filter and high pressure liquid chromatography through a reversed phase C-18 column. APAC was found to be extremely stable to harsh treatments of boiling water for 30 min, acidification to pH 2.0 and proteolytic digestion. A close correlation between activity and iron content of APAC was observed throughout the purification steps. E.S.R. spectrum of APAC showed a resonance line at g = 4.3 in the oxidized from. Peroxide reduction by ascorbate decreased the E.S.R. signal, which reappeared upon reoxidation by H₂O₂. The affinities of APAC to H₂O₂ and ascorbate were high (0.38 mM and 0.2 mM, respectively). Amino acid composition analysis of APAC revealed the presence of glutamic acid: glycine: cysteine residues at 2: 1: 1 ratio.     

Unique properties of the camel erythrocyte membrane: II. Organization of membrane proteins

Camel erythrocyte membranes are distinguished by some unique properties of stability and composition. Notable is their abundance in proteins (protein: lipid ratio of 3 : 1). Membrane proteins of camel erythrocytes were compared with those of human erythrocytes, which have been intensively investigated. Proteins were extracted with various aqueous media (EDTA, alkaline or high ionic strength) and with ionic and non-ionic detergents and were analyzed by gel electrophoresis. In membranes of camel erythrocytes, the peripheral proteins constitute, proportionally, a much smaller fraction of total proteins than in the human erythrocyte, while their distribution is identical per unit of surface area. The camel erythrocyte membrane is particularly rich in integral proteins and in intramembranous particles. The proteins in this membrane are more closely organized than in the human system, as revealed by crosslinking and freeze-etching studies. It is proposed that protein-protein interaction of integral proteins, presumably constituting an “integral skeleton”, is a dominant structural feature stabilizing the camel erythrocyte membrane.     

Phytomelatonin in the leaves and fruits of wild perennial plants

Phytomelatonin has been documented in numerous flowering plants, mostly in cultivated species consumed by humans. Although frugivorous animals feed on fruits, the phytomelatonin content of these organs has hardly ever been tested in wild plants. The aim of this study was to determine the levels of phytomelatonin in the leaves and fleshy fruits of 31 wild perennial species known to be eaten by herbivorous and frugivorous mammals and birds. Considerable levels of phytomelatonin were found in the leaves of all the tested species, and some contained melatonin in their fruits as well. The melatonin content was found to vary significantly in different life forms (trees, shrubs, and climbers), with trees possessing the highest levels. The analysis revealed a significant positive correlation between the phytomelatonin levels in the leaves and the fruits of various species. However, the concentration found in the fruits was generally lower than that found in the leaves of the same species. Despite the presence of phytomelatonin in the fleshy fruits of different families, there was no noticeable common attribute among them. Phytomelatonin was exhibited in both the seeds and the pulp, with no obvious preference for either one. Although it was determined that ingested melatonin enters the bloodstream of birds and mammals, its specific role is still not certain. The potential impact of edible phytomelatonin on the circadian rhythm of herbivores and frugivores is discussed on the basis of these findings.