Contextual specificity in peptide-mediated protein interactions

Most biological processes are regulated through complex networks of transient protein interactions where a globular domain in one protein recognizes a linear peptide from another, creating a relatively small contact interface. Although sufficient to ensure binding, these linear motifs alone are usually too short to achieve the high specificity observed, and additional contacts are often encoded in the residues surrounding the motif (i.e. the context). Here, we systematically identified all instances of peptide-mediated protein interactions of known three-dimensional structure and used them to investigate the individual contribution of motif and context to the global binding energy. We found that, on average, the context is responsible for roughly 20% of the binding and plays a crucial role in determining interaction specificity, by either improving the affinity with the native partner or impeding non-native interactions. We also studied and quantified the topological and energetic variability of interaction interfaces, finding a much higher heterogeneity in the context residues than in the consensus binding motifs. Our analysis partially reveals the molecular mechanisms responsible for the dynamic nature of peptide-mediated interactions, and suggests a global evolutionary mechanism to maximise the binding specificity. Finally, we investigated the viability of non-native interactions and highlight cases of potential cross-reaction that might compensate for individual protein failure and establish backup circuits to increase the robustness of cell networks.     

Cursorial spiders retard initial aphid population growth at low densities in winter wheat

Generalist predators contribute to pest suppression in agroecosystems. Spider communities, which form a substantial fraction of the generalist predator fauna in arable land, are characterized by two functional groups: web-building and cursorial (non-web-building) species. We investigated the relative impact of these two functional groups on a common pest (Sitobion avenae, Aphididae) in wheat by combining a molecular technique that revealed species-specific aphid consumption rates with a factorial field experiment that analyzed the impact, separately and together, of equal densities of these two spider functional groups on aphid population growth. Only cursorial spiders retarded aphid population growth in our cage experiment, but this effect was limited to the initial aphid-population growth period and low-to-intermediate aphid densities. The molecular analysis, which used aphid-specific primers to detect aphid DNA in predator species, detected the highest proportion of aphid-consuming individuals in two cursorial spiders: the foliage-dwelling Xysticus cristatus (Thomisidae) and the ground-active Pardosa palustris (Lycosidae). The results suggest that manipulating the community composition in favour of pest-consuming functional groups may be more important for improving biological control than fostering predator biodiversity per se. Agricultural management practices that specifically foster effective species or functional groups (e.g. mulching for cursorial spiders) should receive more attention in low-pesticide farming systems.     

Facilitative interactions rather than resource partitioning drive diversity-functioning relationships in laboratory fungal communities

We manipulated the number of saprotrophic fungi in either a complex multi-resource substratum (sterilized forest soil), or a single-resource substratum (powdered cellulose). The substrates were inoculated with five common species of soil fungi in all possible combinations (from monocultures to five species in combination). In both substrates, the rate of organic matter decomposition was positively associated with species richness. The effect of fungal diversity was much stronger in the uniform single-resource substrate ( r ² = 0.455, P  < 0.0001) than in soil ( r ² = 0.154, P  < 0.0001). The results document that species richness of microbial decomposers strongly affects decomposition processes, at least at the species poor end of the diversity gradient. Both, 'sampling effect' and 'species complementarity effect' contributed to the community response with the latter being much more pronounced in uniform substrate than in soil. This indicates that facilitative interactions are more important than resource partitioning for positive effects of species richness.     

Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities

Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin (PRN) and hydrogen cyanide (HCN) in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks), as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.     

The role of substrate feeding earthworms (Lumbricidae) for bioturbation in a beechwood soil

Summary Burrow formation (burrow length and faeces production) of the substrate feeding earthworm Aporrectodea caliginosa (Savigny) in relation to three temperatures (5, 10 and 15°C) and soil moisture contents (48, 60 and 73% water of dry wt) was determined. Soil moisture content affected the burrowing activity of A. caliginosa only below a distinct threshold (60% water of dry wt). At sufficient moisture an, increase in temperature by 5° C approximately doubled the amount of egesta produced. Another substrate feeding earthworm (Octolasion lacteum (Örley)) showed a similar pattern of burrowing activity.The data for the dependence of the faeces production of A. caliginosa on soil temperature and moisture content were combined with field data. The amount of faeces produced by the population of this earthworm species in a beechwood on limestone was calculated to be about 4.23 kg ha^-1 a^-1. The amount of egesta produced by all substrate feeding species is assumed to exceed 6 kg ha^-1 a^-1, which is equivalent to a soil layer of approximately 9 mm. This group of earthworms is therefore considered to be of greater importance for bioturbation and the formation of mull than previously assumed.     

Hepatic Rac1 GTPase contributes to liver-mediated basal immune homeostasis and LPS-induced endotoxemia

Background

The Ras-homologous GTPase Rac1 plays a key role in the regulation of gene expression, cytoskeleton-associated processes and cell death as well as carcinogenesis and inflammation. Here, we investigated the impact of Rac1 signaling on liver-mediated immune homeostasis.

Pelagic larvae of New England intertidal gastropods II. Anachis avara

Summary The egg case, pelagic larvae, and young juvenile of Anachis avara Say, a species of prosobranch gastropod belonging to the family Columbellidae, are described and figured from specimes reared in the laboratory.

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Zusammenfassung Die Arbeit beschreibt die Eierkapseln, die pelagischen Larven und die Jugendformen von Anachis avara Say, einer prosobranchen Gastropoden-Spezies, die zur Familie der Columbelliden gehört. Abbildungen von Exemplaren, die im Laboratorium aufgezogen wurden, werden wiedergegeben.

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Contribution number 1341, Woods Hole Oceanographic Institution. This research was supported by N.S.F. grant no. 17883.