On the contribution of water-mediated interactions to protein-complex stability

Protein-water interactions have long been recognized as a major determinant of chain folding, conformational stability, binding specificity and catalysis. However, the detailed effects of water on stabilizing protein-protein interactions remain elusive. A way to test experimentally the contribution of water-mediated interactions is by applying double mutant cycle analysis on pairs of residues that do not form direct interactions, but are bridged by water. Seven such interactions within the interface between TEM1 and BLIP proteins were evaluated. No significant interaction free energy was found between either of them. Water can bridge interactions, but also stabilize the structure of the monomer. To distinguish between these, we performed a bioinformatic analysis using AQUAPROT (http://bioinfo.weizmann.ac.il/aquaprot) to determine the degree of water conservation between the bound and unbound states. 29 structures of twelve complexes and 20 related monomers were analyzed. Of the 262 water molecules located within the interfaces, 145 were conserved between the unbound and bound structures. Strikingly, all 50 buried or partially buried waters in the monomer structures were conserved at the same location in the bound structures. Thus, buried waters have an important role in stabilizing the monomer fold rather than contributing to protein-protein binding, and are not replaced by residues from the incoming protein. Taking together the experimental and bioinformatics evidence suggests that exposed waters within the interface may be good sites for protein engineering, while buried or mostly buried waters should be left unchanged.     

Phylogenetic diversity of bacteria associated with the mucus of Red Sea corals

Coral reefs are the most biodiverse and biologically productive of all marine ecosystems. Corals harbor diverse and abundant prokaryotic communities. However, little is known about the diversity of coral-associated bacterial communities. Mucus is a characteristic product of all corals, forming a coating over their polyps. The coral mucus is a rich substrate for microorganisms. Mucus was collected with a procedure using sterile cotton swabs that minimized contamination of the coral mucus by surrounding seawater. We used molecular techniques to characterize and compare the bacterial assemblages associated with the mucus of the solitary coral Fungia scutaria and the massive coral Platygyra lamellina from the Gulf of Eilat, northern Red Sea. The bacterial communities of the corals F. scutaria and P. lamellina were found to be diverse, with representatives within the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria and Epsilonproteobacteria, as well as the Actinobacteria, Cytophaga-Flavobacter/Flexibacter-Bacteroides group, Firmicutes, Planctomyces, and several unclassified bacteria. However, the total bacterial assemblage of these two corals was different. In contrast to the bacterial communities of corals analyzed in previous studies by culture-based and culture-independent approaches, we found that the bacterial clone libraries of the coral species included a substantial proportion of Actinobacteria. The current study further supports the finding that bacterial communities of coral mucus are diverse.     

Stability in the host-parasitoid relationship of Dialeurodes citri and Encarsia lahorensis in the citrus orchard

The citrus whitefly, Dialeurodes citri (Ashmead), a citrus pest, has been prevalent in Israel since 1975. The parasitic wasp Encarsia lahorensis (Howard) has been successfully used for its biological control since 1980 and thehost-parasitoid system is stable. This studyuses field data from four and a half years inorder to examine whether heterogeneity ofparasitism and risk aggregation can explain thestability. After establishing that theprobability of parasitism is not constant overpatches, we examined the question of parasitoidaggregation, dependent or independent of thehost, at different patch levels. At the treelevel we found an inverse relationship betweenthe proportion of parasitism and host density.At the leaf level, taking the tree effect intoconsideration, the host density dependence wasweak and non-significant. At the leaf level, acombined examination of both types ofheterogeneity in parasite distribution – hostdensity dependent heterogeneity (direct orindirect) and host density independentheterogeneity, was performed using the (CV)² > 1 criterion. The mean (CV)² value over different sampling dateswas greater than one. Host density independentheterogeneity had the greater contribution tostability. The (CV)² findings atleaf level in the plot, combining leaf and treeeffects, represent both aggregation at the treelevel (inverse density dependence) andaggregation at the leaf level (host densityindependence). The heterogeneity findings forparasitoid distribution, together with thestability, which was directly observed, supportour hypothesis that aggregation of risk is animportant mechanism in the stabilisinginteraction between the citrus whitefly and itsspecific parasitoid, E. lahorensis.     

Insecticidal activity of a cryia(c) transgene in callus derived from regeneration-recalcitrant cotton (Gossypium hirsutum L.)

Summary The insecticidal effectiveness of a δ-endotoxin Cry protein from Bacillus thuringiensis in non-regenerable callus of a commercial Gossypium hirsutum L. variety was investigated. Two transgenic callus types were generated. The first callus type harbored the cry1A(c) gene and the hygromycin B phosphotransferase hpt selectable marker gene. The second callus type, the transgenic control, carried the marker genes β-glucuronidase (GUS) and hpt. Growth and survival rates of three major cotton moth species, Pectinophora gossypiella, Helicoverpa armigera, and Spodoptera littoralis, were examined with aseptic neonates reared on callus. Normal larval development occurred in all species supplied with non-transgenic callus, but insects died, or their growth was severely restricted, when reared on transgenic callus harvested from hygromycin B-supplemented medium. Development of larvae on transgenic control and on non-transgenic callus became very much alike after the transgenic control tissue had been subcultured on a hygromyein B-free medium for about 100 d prior to the insect-callus bioassay. Accordingly, for detection of Bt toxin activity without the interference of the influence of hygromycin B on insects, cry1A(c) callus was infested with insects after it had been propagated for more than 100 d on a medium free of the antibiotic. Under these experimental conditions all P. gossypiella and H. armigera, and most S. littoralis neonates died, and the growth (e.g., weight increment) of S. littoralis survivors was markedly impeded by cry1A(c) callus. Three new findings emerge from this study: first, P. gossypiella, a pest feeding in the field on bolls only, can be grown in vitro on cotton callus; second, in a host which is recalcitrant in terms of plant regeneration, the biological potency of an insectdetrimental transgene can nevertheless be evaluated by generating a transgenic host callus and conducting in vitro transgenic callus-insect assays; and third, our results suggest that hygromycin B is toxic to lepidopteran larvae.     

Analysis of hystereses in force length and force calcium relations

Analysis of the hystereses in the force-length relationship at constant Ca(2+) concentration and in the force-calcium relationship at constant sarcomere length (SL) provides insight into the mechanisms that control cross-bridge (XB) recruitment. The hystereses are related here to two mechanisms that regulate the number of strong XBs: the cooperativity, whereby the number of strong XBs determines calcium affinity, and the mechanical feedback, whereby the shortening velocity determines the duration for which the XBs are in the strong state. The study simulates the phenomena and defines the role of these feedbacks. The model that couples calcium kinetics with XB cycling was built on Simulink software (Matlab). Counterclockwise (CCW) hysteresis, wherein the force response lags behind the SL oscillations, at a constant calcium level, is obtained in the force-length plane when neglecting the mechanical feedback and accounting only for the cooperativity mechanism. Conversely, the force response precedes the SL oscillations, yielding a clockwise (CW) hysteresis when only the mechanical feedback is allowed to exist. In agreement with experimental observations, either CW or CCW hysteresis is obtained when both feedbacks coexist: CCW hystereses are obtained at low frequencies (<3 Hz), and the direction is reversed to CW at higher frequencies (>3 Hz). The cooperativity dominates at low frequencies and allows the muscle to adapt XB recruitment to slow changes in the loading conditions. The changeover frequency from CCW to CW hysteresis defines the velocity limit above which the muscle absorbs rather than generates energy. The hysteresis in the force-calcium relation is conveniently explained by the same cooperativity mechanism. We propose that a single cooperativity mechanism that depends on the number of strong XBs can explain the hystereses in the force-length as well as in the force-calcium relationships.     

Fractionation of the three stable oxygen isotopes by oxygen-producing and oxygen-consuming reactions in photosynthetic organisms

The triple isotope composition (delta17O and delta18O) of dissolved O2 in the ocean and in ice cores was recently used to assess the primary productivity over broad spatial and temporal scales. However, assessment of the productivity with the aid of this method must rely on accurate measurements of the 17O/16O versus 18O/16O relationship in each of the main oxygen-producing and -consuming reactions. Data obtained here showed that cleavage of water in photosystem II did not fractionate oxygen isotopes; the delta18O and delta17O of the O2 evolved were essentially identical to those of the substrate water. The fractionation slopes for the oxygenase reaction of Rubisco and respiration were identical (0.518 +/- 0.001) and that of glycolate oxidation was 0.503 +/- 0.002. There was a considerable difference in the slopes of O2 photoreduction (the Mehler reaction) in the cyanobacterium Synechocystis sp. strain PCC 6803 (0.497 +/- 0.004) and that of pea (Pisum sativum) thylakoids (0.526 +/- 0.001). These values provided clear and independent evidence that the mechanism of O2 photoreduction differs between higher plants and cyanobacteria. We used our method to assess the magnitude of O2 photoreduction in cyanobacterial cells maintained under conditions where photorespiration was negligible. It was found that electron flow to O2 can be as high as 40% that leaving photosystem II, whereas respiratory activity in the light is only 6%. The implications of our findings to the evaluation of specific O2-producing or -consuming reactions, in vivo, are discussed.     

Evolution under domestication: contrasting functional morphology of seedlings in domesticated cassava and its closest wild relatives

Although cassava (Manihot esculenta ssp. esculenta) is asexually propagated, farmers incorporate plants from seedlings into planting stocks. These products of sex are exposed to selection, which in agricultural environments should favour rapid growth. To examine whether seedling morphology has evolved under domestication, we compared domesticated cassava, its wild progenitor (M. esculenta ssp. flabellifolia) and their sister species (M. pruinosa) under controlled conditions. Field observations complemented laboratory study. In both wild taxa, the hypocotyl did not elongate (hypogeal germination) and cotyledons remained enclosed in the testa. In domesticated cassava, the hypocotyl elongated (epigeal germination), and cotyledons emerged and became foliaceous. The difference in hypocotyl elongation was fixed, whereas cotyledon morphology varied with environmental conditions in M. pruinosa. Comparative analysis suggests that epigeal germination is primitive in Manihot, that the lineage including wild ancestors of cassava evolved hypogeal germination--which confers greater tolerance to risks in their savanna environment--and that with domestication, there was a reversion to epigeal germination and photosynthetic cotyledons, traits conferring high initial growth rates in agricultural habitats.