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RNase MRP is an essential eukaryotic ribonucleoprotein complex involved in the maturation of rRNA and the regulation of the cell cycle. RNase MRP is related to the ribozyme-based RNase P, but it has evolved to have distinct cellular roles. We report a cryo-EM structure of the S. cerevisiae RNase MRP holoenzyme solved to 3.0 Å. We describe the structure of this 450 kDa complex, interactions between its components, and the organization of its catalytic RNA. We show that some of the RNase MRP proteins shared with RNase P undergo an unexpected RNA-driven remodeling that allows them to bind to divergent RNAs. Further, we reveal how this RNA-driven protein remodeling, acting together with the introduction of new auxiliary elements, results in the functional diversification of RNase MRP and its progenitor, RNase P, and demonstrate structural underpinnings of the acquisition of new functions by catalytic RNPs. Ribozyme-based RNase MRP is an essential eukaryotic enzyme involved in the maturation of rRNA and is evolutionarily related to RNase P. Here, the authors present the 3.0 Å cryo-EM structure of the S. cerevisiae RNase MRP holoenzyme, a 450 kDa ribonucleoprotein complex and compare it with RNase P.

Transfer RNA (tRNA) is produced as a precursor molecule that needs to be processed at its 3′ and 5′ ends. Ribonuclease P is the sole endonuclease responsible for processing the 5′ end of tRNA by cleaving the precursor and leading to tRNA maturation. It was one of the first catalytic RNA molecules identified 1 and consists of a single RNA component in all organisms and only one protein component in bacteria. It is a true multi-turnover ribozyme and one of only two ribozymes (the other being the ribosome) that are conserved in all kingdoms of life. Here we show the crystal structure at 3.85 Å resolution of the RNA component of Thermotoga maritima ribonuclease P. The entire RNA catalytic component is revealed, as well as the arrangement of the two structural domains. The structure shows the general architecture of the RNA molecule, the inter- and intra-domain interactions, the location of the universally conserved regions, the regions involved in pre-tRNA recognition and the location of the active site. A model with bound tRNA is in agreement with all existing data and suggests the general basis for RNA–RNA recognition by this ribozyme.

Ribonuclease (RNase) P is a site‐specific endoribonuclease found in all kingdoms of life. Typical RNase P consists of a catalytic RNA component and a protein moiety. In the eukaryotes, the RNase P lineage has split into two, giving rise to a closely related enzyme, RNase MRP, which has similar components but has evolved to have different specificities. The eukaryotic RNases P/MRP have acquired an essential helix‐loop‐helix protein‐binding RNA domain P3 that has an important function in eukaryotic enzymes and distinguishes them from bacterial and archaeal RNases P. Here, we present a crystal structure of the P3 RNA domain from Saccharomyces cerevisiae RNase MRP in a complex with RNase P/MRP proteins Pop6 and Pop7 solved to 2.7 Å. The structure suggests similar structural organization of the P3 RNA domains in RNases P/MRP and possible functions of the P3 domains and proteins bound to them in the stabilization of the holoenzymes' structures as well as in interactions with substrates. It provides the first insight into the structural organization of the eukaryotic enzymes of the RNase P/MRP family.

RNase P is the only endonuclease responsible for processing the 5′ end of transfer RNA by cleaving a precursor and leading to tRNA maturation 1 , 2 . It contains an RNA component and a protein component and has been identified in all organisms. It was one of the first catalytic RNAs identified 3 and the first that acts as a multiple-turnover enzyme in vivo . RNase P and the ribosome are so far the only two ribozymes known to be conserved in all kingdoms of life. The RNA component of bacterial RNase P can catalyse pre-tRNA cleavage in the absence of the RNase P protein in vitro and consists of two domains: a specificity domain and a catalytic domain 4 , 5 . Here we report a 3.15-Å resolution crystal structure of the 154-nucleotide specificity domain of Bacillus subtilis RNase P. The structure reveals the architecture of this domain, the interactions that maintain the overall fold of the molecule, a large non-helical but well-structured module that is conserved in all RNase P RNA, and the regions that are involved in interactions with the substrate.

Large RNA molecules, such as ribozymes, fold with well-defined tertiary structures that are important for their activity. There are many instances of ribozymes with identical function but differences in their secondary structures, suggesting alternative tertiary folds. Here, we report a crystal structure of the 161-nucleotide specificity domain of an A-type ribonuclease P that differs in secondary and tertiary structure from the specificity domain of a B-type molecule. Despite the differences, the cores of the domains have similar three-dimensional structure. Remarkably, the similar geometry of the cores is stabilized by a different set of interactions involving distinct auxiliary elements.

RNase MRP is an essential eukaryotic ribonucleoprotein complex involved in the maturation of rRNA and the regulation of the cell cycle. RNase MRP is related to the ribozyme-based RNase P, but it has evolved to have distinct cellular roles. We report a cryo-EM structure of the S. cerevisiae RNase MRP holoenzyme solved to 3.0 A. We describe the structure of this 450 kDa complex, interactions between its components, and the organization of its catalytic RNA. We show that while the catalytic center of RNase MRP is inherited from the ancestral enzyme RNase P, the substrate binding pocket of RNase MRP is significantly altered by the addition of unique RNA and protein elements, as well as by RNA-driven protein remodeling.

Annually, up to 15 million tons of coffee production waste are produced worldwide. Among them are spent coffee grounds (SCG), which have the potential to be recycled and used as organic fertilizers. However, their direct application to soil is limited due to the presence of ecotoxic compounds (phenols, tannins, and caffeine). Composting is a promising approach; however, the highly variable properties of the raw coffee materials require the selection of optimal production and application modes. In this study, we performed two composting methods for SCG, i.e., vermicomposting and microbial composting, in mixtures with co-composting substrate at five SCG/substrate ratios (0, 25, 50, 75, and 100% SCG). First, the acute toxicity of raw SGC and its mixtures to earthworm Eisenia andrei was evaluated. After 30 days of composting, chemical and microbiological properties, including pH, RedOx potential (Eh), organic carbon (C[sub.org]), lignin content, bacteria count, diversity, and potential metabolic activity, were determined in the end products. As composting went on, the pH increased from 5.6–6.2 to 6.0–7.3 and 7.4–7.7 under microbial composting and vermicomposting, respectively. RedOx potential levels achieved 142–166 mV for microbial composting and 73–113 mV for vermicomposting. Organic matter (OM) content reached 86–94%, with an increasing proportion of lignin, demonstrating the decomposition of more readily accessible organic matter. Vermicomposting and microbial composting produced chemically safe and microbiologically highly active composts. An initial SCG content of 25–50% of the compost mixture’s weight yielded the most favorable properties for the resulting compost (high organic matter content and optimal pH levels). Due to the high biological activity of both composting methods, the resultant composts are likely to have a positive effect on plant growth and development and soil health when used as organic nutrient resources.

Acute shortage of water resources and high unproductive water losses are the key problems of irrigated agriculture in arid regions. One of the possible solutions is to optimize soil water retention using natural and synthetic polymer water absorbers. Our approach uses the HYDRUS-1D design to optimize the placement of organic water absorbents such as peat and composite hydrogels in the soil profile in the form of water-storing capillary barriers. Field testing of the approach used a water balance greenhouse experiment with the cultivation of butternut squash (butternut squash (Cucurbita moschata (Duchesne, 1786)) under sprinkler irrigation with measurement of the soil moisture profile and unproductive water losses in the form of lysimetric water outflow. In addition, the biodegradation rate of organic water absorbents was studied at the soil surface and at a depth of 20 cm. Organic capillary barriers reduced unproductive water losses by 40–70%, retaining water in the topsoil and increasing evapotranspiration by 70–130% with a corresponding increase in plant biomass and fruit yield. The deepening of organic soil modifiers to the calculated depth not only allowed capillary barriers to form, but also prevented their biodegradation. The best results in soil water retention, plant growth and yield according to the “dose-effect” criterion were obtained for a composite superabsorbent with peat filling of an acrylic polymer matrix. The study showed good compliance between the HYDRUS design and the actual efficiency of capillary barriers as an innovative technology for irrigated agriculture using natural and synthetic water absorbents.

This article describes the digital twin of power drive unit (engine and transmission) of 8-ton class wheel tractor with automatic gearbox. Detailed mathematical model of considered tractor power drive unit - engine with 16-speed automatic gearbox and friction shift of stages under load without breaking the power flow is given. The theoretical methods of research are based on the use of the MATLab package. With the help of fundamental package units, models of gearbox physical components are created: friction clutches, gears, shafts with the required properties, engine mathematical model, as well as model of the transmission control system. The calculation methods of the gearbox dynamic processes going on in the gear shifts using friction clutches is proposed. A feature of the mathematical model is consideration of the resistive torque, the rate of rise of switched on clutches friction torque, both during switching to the higher and lower gears. Mathematic simulation of tractor power drive unit operation under load was performed. The results of the completed calculations are presented. The possibility of using this digital model to simulate tractor operation during its main work operations is shown.