Reconstitution of Targeted Deadenylation by the Ccr4-Not Complex and the YTH Domain Protein Mmi1

SummaryCcr4-Not is a conserved protein complex that shortens the 3′ poly(A) tails of eukaryotic mRNAs to regulate transcript stability and translation into proteins. RNA-binding proteins are thought to facilitate recruitment of Ccr4-Not to certain mRNAs, but lack of an in-vitro-reconstituted system has slowed progress in understanding the mechanistic details of this specificity. Here, we generate a fully recombinant Ccr4-Not complex that removes poly(A) tails from RNA substrates. The intact complex is more active than the exonucleases alone and has an intrinsic preference for certain RNAs. The RNA-binding protein Mmi1 is highly abundant in preparations of native Ccr4-Not. We demonstrate a high-affinity interaction between recombinant Ccr4-Not and Mmi1. Using in vitro assays, we show that Mmi1 accelerates deadenylation of target RNAs. Together, our results support a model whereby both RNA-binding proteins and the sequence context of mRNAs influence deadenylation rate to regulate gene expression

Forest-derived lignin biomarkers in an Australian oxisol decrease substantially after 90 years of pasture

The dynamics of soil organic matter are a key factor in controlling the terrestrial carbon cycle. Compound specific stable carbon isotope analysis has given new insight in to the stability of individual organic molecules in soil. For lignin, one of the major plant compounds, available data suggest the existence of both a labile (turnover time <1 year) and a relatively stable (turnover time in the range of decades) pool. However, these data derive almost exclusively from agricultural soils in temperate climates. In order to extend the range both in ecosystem type and observed time span, we analysed a pasture soil in subtropical Australia that had experienced a land use change from rainforest 90 years earlier. We determined the concentration and isotopic signature of lignin biomarkers and compared them to those in an existing rainforest soil nearby and to samples of the respective vegetation. The land use change shifted both the relative abundance of lignin biomarkers and their isotopic signatures. In particular, the isotope data indicate that the pasture soil contains only small proportions of inherited rainforest-derived lignin biomarkers, which are mostly close to or below detection limit. These drastic changes in biomarker composition indicate that the original lignin structure had little chance to persist in this soil over a century. Thus, the stable soil organic carbon identified an earlier study of this soil is probably highly altered material and lignin biomarkers are not a suitable proxy of this stable carbon

Microplastics in arctic invertebrates- Status on occurrence and recommendations for future monitoring

Few studies have been published on occurrence and distribution on microplastics (MPs) in invertebrates from the Arctic. We still need to develop harmonised methods to enable good comparison between studies taking into account recovery rates, size ranges, shapes and polymer types. Here, we review studies on MPs in invertebrates from the Arctic and present suggestions on sampling protocols and potential indicator species. Since information on MPs in Arctic invertebrates is vastly lacking, we recommend to at least include suspension feeding bivalves like mussels in monitoring programmes to function as indicator species in the Arctic. Mussels have also been suggested as indicator species for MP monitoring in coastal regions further south. Although we recognise the challenge with particle selection and egestion in mussels as well as the relatively low concentrations of MPs in Arctic waters, uptake levels seem to represent recent exposures. More research is needed to understand these selection processes and how they affect the bioaccumulation processes. Future research should include studies on whether different functional groups of invertebrates have different exposures to MPs, e.g., if there are differences between sessile versus motile species or different feeding strategies. More knowledge on monitoring strategies for pelagic and benthic species is needed.Microplastics in arctic invertebrates- Status on occurrence and recommendations for future monitoringpublishedVersio

Architecture of soil microaggregates: Advanced methodologies to explore properties and functions

The functions of soils are intimately linked to their three-dimensional pore space and the associated biogeochemical interfaces, mirrored in the complex structure that developed during pedogenesis. Under stress overload, soil disintegrates into smaller compound structures, conventionally named aggregates. Microaggregates (<250 µm) are recognized as the most stable soil structural units. They are built of mineral, organic, and biotic materials, provide habitats for a vast diversity of microorganisms, and are closely involved in the cycling of matter and energy. However, exploring the architecture of soil microaggregates and their linkage to soil functions remains a challenging but demanding scientific endeavor. With the advent of complementary spectromicroscopic and tomographic techniques, we can now assess and visualize the size, composition, and porosity of microaggregates and the spatial arrangement of their interior building units. Their combinations with advanced experimental pedology, multi-isotope labeling experiments, and computational approaches pave the way to investigate microaggregate turnover and stability, explore their role in element cycling, and unravel the intricate linkage between structure and function. However, spectromicroscopic techniques operate at different scales and resolutions, and have specific requirements for sample preparation and microaggregate isolation; hence, special attention must be paid to both the separation of microaggregates in a reproducible manner and the synopsis of the geography of information that originates from the diverse complementary instrumental techniques. The latter calls for further development of strategies for synlocation and synscaling beyond the present state of correlative analysis. Here, we present examples of recent scientific progress and review both options and challenges of the joint application of cutting-edge techniques to achieve a sophisticated picture of the properties and functions of soil microaggregates

The C:N:P:S stoichiometry of soil organic matter

The formation and turnover of soil organic matter (SOM) includes the biogeochemical processing of the macronutrient elements nitrogen (N), phosphorus (P) and sulphur (S), which alters their stoichiometric relationships to carbon (C) and to each other. We sought patterns among soil organic C, N, P and S in data for c. 2000 globally distributed soil samples, covering all soil horizons. For non-peat soils, strong negative correlations (p < 0.001) were found between N:C, P:C and S:C ratios and % organic carbon (OC), showing that SOM of soils with low OC concentrations (high in mineral matter) is rich in N, P and S. The results can be described approximately with a simple mixing model in which nutrient-poor SOM (NPSOM) has N:C, P:C and S:C ratios of 0.039, 0.0011 and 0.0054, while nutrient-rich SOM (NRSOM) has corresponding ratios of 0.12, 0.016 and 0.016, so that P is especially enriched in NRSOM compared to NPSOM. The trends hold across a range of ecosystems, for topsoils, including O horizons, and subsoils, and across different soil classes. The major exception is that tropical soils tend to have low P:C ratios especially at low N:C. We suggest that NRSOM comprises compounds selected by their strong adsorption to mineral matter. The stoichiometric patterns established here offer a new quantitative framework for SOM classification and characterisation, and provide important constraints to dynamic soil and ecosystem models of carbon turnover and nutrient dynamics

The study of atmospheric ice-nucleating particles via microfluidically generated droplets

Ice-nucleating particles (INPs) play a significant role in the climate and hydrological cycle by triggering ice formation in supercooled clouds, thereby causing precipitation and affecting cloud lifetimes and their radiative properties. However, despite their importance, INP often comprise only 1 in 10³–10⁶ ambient particles, making it difficult to ascertain and predict their type, source, and concentration. The typical techniques for quantifying INP concentrations tend to be highly labour-intensive, suffer from poor time resolution, or are limited in sensitivity to low concentrations. Here, we present the application of microfluidic devices to the study of atmospheric INPs via the simple and rapid production of monodisperse droplets and their subsequent freezing on a cold stage. This device offers the potential for the testing of INP concentrations in aqueous samples with high sensitivity and high counting statistics. Various INPs were tested for validation of the platform, including mineral dust and biological species, with results compared to literature values. We also describe a methodology for sampling atmospheric aerosol in a manner that minimises sampling biases and which is compatible with the microfluidic device. We present results for INP concentrations in air sampled during two field campaigns: (1) from a rural location in the UK and (2) during the UK’s annual Bonfire Night festival. These initial results will provide a route for deployment of the microfluidic platform for the study and quantification of INPs in upcoming field campaigns around the globe, while providing a benchmark for future lab-on-a-chip-based INP studies

Structural and biochemical characterization of the human SKI complex

The eukaryotic RNA-degrading exosome is universally present in nuclear and cytoplasmic cellular compartments and is involved in wide-spread RNA processing and degradation functions that rely on its 3'-5' RNA exonuclease activity. In the cytoplasm, it associates with the Ski complex via the Ski7 protein to function in mRNA turnover and surveillance pathways. As part of the Ski complex, together with the Ski3 and Ski8 proteins, the DExH helicase Ski2 binds and threads RNA to the exosome for degradation. The collaboration of the respective helicase and nuclease activities is conserved in eukaryotes and has been well studied in S. cerevisiae, but major questions regarding the molecular mechanisms of its regulation and unwinding activity remain open. In this dissertation, we solved several cryo-EM structures of the human SKI (hSKI) complex in a resting state in absence of a substrate, in a substrate-binding but inactive state and in an active substrate-working state and uncovered the existence of two fundamentally different activity-related conformations. The open and closed conformations, are characterized by the detachment of the hSKI2 helicase core from the complex. In the closed state, the hSKI3 protein blocks the RNA exit site of the hSKI2 helicase like a gate to prevent threading of the substrate. In the open conformation, when the hSKI2 helicase is detached from the complex, the RNA exit site is free, allowing substrate translocation. When analyzed bound to the 80S ribosome, the inactive hSKI complex recognizes short RNA 3' overhangs at the mRNA entry site in the closed conformation. The activation of the complex the detaches the hSKI2 helicase and efficiently extracts RNA from the mRNA entry site of the ribosome. The crystal structure of the S. cerevisiae Ski7-bound cytoplasmic exosome shows the interaction of Ski7 with a conserved binding interface with the nuclear exosome adaptor Rrp6. Knowing the precise mode of interaction between Ski7 and the exosome, we identified a human Ski7-like protein in a splicing variant of the HBS1L protein that bridges the interaction between the hSKI complex and the human cytoplasmic exosome. In subsequent biochemical experiments, we further verified its function and study the RNA channeling capabilities of the hSKI-exosome holocomplex. We conclude that RNA channeling to the cytoplasmic exosome requires the open conformation of hSKI and that RNA channeling between the two complexes follows a conserved principle similar to the nuclear Mtr4-exosome holocomplex. In addition, the analysis and comparison to the homologous S. cerevisiae Ski complex allowed us to identify common principles of regulation with respect to the closed and open conformational states but also spots differences with respect to the auto-inhibition previously described in the S. cerevisiae complex. The findings of this dissertation give unique insight into the molecular mechanisms of the human SKI complex and change the current understanding of how it functions together with the exosome to degrade mRNAs in the cytoplasm. These insights furthermore set the basis to begin to understand how hSKI-related mutations give rise to human disease

Organic soybeans – Managing quality from field to feeding

Soybeans are rich in protein and have a well-balanced amino acid profile. Since soya fits well for many farms in Europe, it provides also an option for farmers to grow their own feed. By doing so, they can increase the added value on their farms and can respond to the demand of consumers for regional food products. The brochure is intended to help keep the quality of the soya bean as high as possible, from sowing to harvesting and storage, from thermal processing to feeding poultry and pigs. In addition, special attention is paid to compliance with organic quality. The brochure includes a checklist of the main key practice points and portrays three integrated organic farms in Germany