Defining the Specificity of Cotranslationally Acting Chaperones by Systematic Analysis of mRNAs Associated with Ribosome-Nascent Chain Complexes

Polypeptides exiting the ribosome must fold and assemble in the crowded environment of the cell. Chaperones and other protein homeostasis factors interact with newly translated polypeptides to facilitate their folding and correct localization. Despite the extensive efforts, little is known about the specificity of the chaperones and other factors that bind nascent polypeptides. To address this question we present an approach that systematically identifies cotranslational chaperone substrates through the mRNAs associated with ribosome-nascent chain-chaperone complexes. We here focused on two Saccharomyces cerevisiae chaperones: the Signal Recognition Particle (SRP), which acts cotranslationally to target proteins to the ER, and the Nascent chain Associated Complex (NAC), whose function has been elusive. Our results provide new insights into SRP selectivity and reveal that NAC is a general cotranslational chaperone. We found surprising differential substrate specificity for the three subunits of NAC, which appear to recognize distinct features within nascent chains. Our results also revealed a partial overlap between the sets of nascent polypeptides that interact with NAC and SRP, respectively, and showed that NAC modulates SRP specificity and fidelity in vivo. These findings give us new insight into the dynamic interplay of chaperones acting on nascent chains. The strategy we used should be generally applicable to mapping the specificity, interplay, and dynamics of the cotranslational protein homeostasis network

Short- and long-term effects of continuous compost amendment on soil microbiome community

Organic amendment, and especially the use of composts, is a well-accepted sustainable agricultural practice. Compost increases soil carbon and microbial biomass, changes enzymatic activity, and enriches soil carbon and nitrogen stocks. However, relatively little is known about the immediate and long-term temporal dynamics of agricultural soil microbial communities following repeated compost applications. Our study was conducted at two field sites: Newe Ya'ar (NY, Mediterranean climate) and Gilat (G, semi-arid climate), both managed organically over 4 years under either conventional fertilization (0, zero compost) or three levels of compost amendment (20, 40 and 60 m3/ha or 2, 4, 6 L/m2). Microbial community dynamics in the soils was examined by high- and low-time-resolution analyses. Annual community composition in compost-amended soils was significantly affected by compost amendment levels in G (first, second and third years) and in NY (third year). Repeated sampling at high resolution (9–10 times over 1 year) showed that at both sites, compost application initially induced a strong shift in microbial communities, lasting for up to 1 month, followed by a milder response. Compost application significantly elevated alpha diversity at both sites, but differed in the compost–dose correlation effect. We demonstrate higher abundance of taxa putatively involved in organic decomposition and characterized compost-related indicator taxa and a compost-derived core microbiome at both sites. Overall, this study describes temporal changes in the ecology of soil microbiomes in response to compost vs. conventional fertilization

Microbial Consortia versus Single-Strain Inoculants: An Advantage in PGPM-Assisted Tomato Production?

The use of biostimulants with plant growth-promoting properties, but without significant input of nutrients, is discussed as a strategy to increase stress resistance and nutrient use efficiency of crops. However, limited reproducibility under real production conditions remains a major challenge. The use of combination products based on microbial and non-microbial biostimulants or microbial consortia, with the aim to exploit complementary or synergistic interactions and increase the flexibility of responses under different environmental conditions, is discussed as a potential strategy to overcome this problem. This study aimed at comparing the efficiency of selected microbial single-strain inoculants with proven plant-growth promoting potential versus consortium products under real production conditions in large-scale tomato cultivation systems, exposed to different environmental challenges. In a protected greenhouse production system at Timisoara, Romania, with composted cow manure, guano, hair-, and feather-meals as major fertilizers, different fungal and bacterial single-strain inoculants, as well as microbial consortium products, showed very similar beneficial responses. Nursery performance, fruit setting, fruit size distribution, seasonal yield share, and cumulative yield (39⁻84% as compared to the control) were significantly improved over two growing periods. By contrast, superior performance of the microbial consortia products (MCPs) was recorded under more challenging environmental conditions in an open-field drip-fertigated tomato production system in the Negev desert, Israel with mineral fertilization on a high pH (7.9), low fertility, and sandy soil. This was reflected by improved phosphate (P) acquisition, a stimulation of vegetative shoot biomass production and increased final fruit yield under conditions of limited P supply. Moreover, MCP inoculation was associated with selective changes of the rhizosphere-bacterial community structure particularly with respect to Sphingobacteriia and Flavobacteria, reported as salinity indicators and drought stress protectants. Phosphate limitation reduced the diversity of bacterial populations at the root surface (rhizoplane) and this effect was reverted by MCP inoculation, reflecting the improved P status of the plants. The results support the hypothesis that the use of microbial consortia can increase the efficiency and reproducibility of BS-assisted strategies for crop production, particularly under challenging environmental conditions

Friendship, Justice, and Aristotle: Some Reasons to Be Sceptical

It is sometimes held that modern institutionally-focussed conceptions of social justice are lacking in one essential respect: they ignore the importance of civic friendship or solidarity. It is also, typically simultaneously, held that Aristotle's thought provides a fertile ground for elucidating an account of civic friendship. I argue, first, that Aristotle is no help on this score: he has no conception of distinctively civic friendship. I then go on to argue that the Kantian distinction between perfect and imperfect duties is more useful than talk of civic friendship in capturing the non-institutional demands of social justice