Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes

Betacoronaviruses are a genus within the Coronaviridae family of RNA viruses. They are capable of infecting vertebrates and causing epidemics as well as global pandemics in humans. Mitigating the threat posed by Betacoronaviruses requires an understanding of their molecular diversity. The development of novel antivirals hinges on understanding the key regulatory elements within the viral RNA genomes, in particular the 5'-proximal region, which is pivotal for viral protein synthesis. Using a combination of cryo-electron microscopy, atomic force microscopy, chemical probing, and computational modeling, we determined the structures of 5'-proximal regions in RNA genomes of Betacoronaviruses from four subgenera: OC43-CoV, SARS-CoV-2, MERS-CoV, and Rousettus bat-CoV. We obtained cryo-electron microscopy maps and determined atomic-resolution models for the stem-loop-5 (SL5) region at the translation start site and found that despite low sequence similarity and variable length of the helical elements it exhibits a remarkable structural conservation. Atomic force microscopy imaging revealed a common domain organization and a dynamic arrangement of structural elements connected with flexible linkers across all four Betacoronavirus subgenera. Together, these results reveal common features of a critical regulatory region shared between different Betacoronavirus RNA genomes, which may allow targeting of these RNAs by broad-spectrum antiviral therapeutics.

Despite the odds: formation of the SARS-CoV-2 methylation complex

Coronaviruses modify their single-stranded RNA genome with a methylated cap during replication to mimic the eukaryotic mRNAs. The capping process is initiated by several nonstructural proteins (nsp) encoded in the viral genome. The methylation is performed by two methyltransferases, nsp14 and nsp16, while nsp10 acts as a co-factor to both. Additionally, nsp14 carries an exonuclease domain which operates in the proofreading system during RNA replication of the viral genome. Both nsp14 and nsp16 were reported to independently bind nsp10, but the available structural information suggests that the concomitant interaction between these three proteins would be impossible due to steric clashes. Here, we show that nsp14, nsp10, and nsp16 can form a heterotrimer complex upon significant allosteric change. This interaction is expected to encourage the formation of mature capped viral mRNA, modulating nsp14's exonuclease activity, and protecting the viral RNA. Our findings show that nsp14 is amenable to allosteric regulation and may serve as a novel target for therapeutic approaches.

miR-125b-5p impacts extracellular vesicle biogenesis, trafficking, and EV subpopulation release in the porcine trophoblast by regulating ESCRT-dependent pathway

Intercellular communication is a critical process that ensures cooperation between distinct cell types at the embryo-maternal interface. Extracellular vesicles (EVs) are considered to be potent mediators of this communication by transferring biological information in their cargo (e.g., miRNAs) to the recipient cells. miRNAs are small non-coding RNAs that affect the function and fate of neighboring and distant cells by regulating gene expression. Focusing on the maternal side of the dialog, we recently revealed the impact of embryonic signals, including miRNAs, on EV-mediated cell-to-cell communication. In this study, we show the regulatory mechanism of the miR-125b-5p ESCRT-mediated EV biogenesis pathway and the further secretion of EVs by trophoblasts at the time when the crucial steps of implantation are taking place. To test the ability of miR-125b-5p to influence the expression of genes involved in the generation and release of EV subpopulations in porcine conceptuses, we used an ex vivo approach. Next, in silico and in vitro analyses were performed to confirm miRNA-mRNA interactions. Finally, EV trafficking and release were assessed using several imaging and particle analysis tools. Our results indicated that conceptus development and implantation are accompanied by changes in the abundance of EV biogenesis and trafficking machinery. ESCRT-dependent EV biogenesis and the further secretion of EVs were modulated by miR-125b-5p, specifically impacting the ESCRT-II complex (via VPS36) and EV trafficking in primary porcine trophoblast cells. The identified miRNA-ESCRT interplay led to the generation and secretion of specific subpopulations of EVs. miRNA present at the embryo-maternal interface governs EV-mediated communication between the mother and the developing conceptus, leading to the generation, trafficking, and release of characteristic subpopulations of EVs.

Cryo-EM structure of human eIF5A-DHS complex reveals the molecular basis of hypusination-associated neurodegenerative disorders

Hypusination is a unique post-translational modification of the eukaryotic translation factor 5A (eIF5A) that is essential for overcoming ribosome stalling at polyproline sequence stretches. The initial step of hypusination, the formation of deoxyhypusine, is catalyzed by deoxyhypusine synthase (DHS), however, the molecular details of the DHS-mediated reaction remained elusive. Recently, patient-derived variants of DHS and eIF5A have been linked to rare neurodevelopmental disorders. Here, we present the cryo-EM structure of the human eIF5A-DHS complex at 2.8 Å resolution and a crystal structure of DHS trapped in the key reaction transition state. Furthermore, we show that disease-associated DHS variants influence the complex formation and hypusination efficiency. Hence, our work dissects the molecular details of the deoxyhypusine synthesis reaction and reveals how clinically-relevant mutations affect this crucial cellular process.

Cryo-EM structure of the fully assembled Elongator complex

Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA anticodons are directly influencing ribosome decoding and dynamics during translation elongation and are crucial for maintaining proteome integrity. In eukaryotes, wobble uridines are modified by Elongator, a large and highly conserved macromolecular complex. Elongator consists of two subcomplexes, namely Elp123 containing the enzymatically active Elp3 subunit and the associated Elp456 hetero-hexamer. The structure of the fully assembled complex and the function of the Elp456 subcomplex have remained elusive. Here, we show the cryo-electron microscopy structure of yeast Elongator at an overall resolution of 4.3 Å. We validate the obtained structure by complementary mutational analyses in vitro and in vivo. In addition, we determined various structures of the murine Elongator complex, including the fully assembled mouse Elongator complex at 5.9 Å resolution. Our results confirm the structural conservation of Elongator and its intermediates among eukaryotes. Furthermore, we complement our analyses with the biochemical characterization of the assembled human Elongator. Our results provide the molecular basis for the assembly of Elongator and its tRNA modification activity in eukaryotes.

Chiral and structural polymorphism of fibril architectures of homologous lysozymes

Amyloid fibrils are fascinating and complex structures with the multilayered chiral organization. Using the multimodal methodology, including VCD, ECD, cryo-EM, and TEM, we characterized in detail different levels of organization (secondary structure/protofilament/mesoscopic structure) of amyloid fibrils prepared from proteins highly homologous in structure (hen egg white and human lysozymes). Our results demonstrate that small changes in the native protein structure or preparation conditions translate into significant differences in the handedness and architecture of the formed fibrils at various levels of their complexity. In particular, fibrils of hen egg white and human lysozymes obtained in vitro at the same preparation conditions, possess different secondary structure, protofilament twist and ultrastructure. Yet, formed fibrils adopted a relatively similar mesoscopic structure, as observed in high-resolution 3D cryo-EM, scarcely used up to now for fibrils obtained in vitro in denaturing condition. Our results add to other puzzling experiments implicating the indeterministic nature of fibril formation.

High-resolution cryo-EM structures of plant cytochrome b6f at work

Plants use solar energy to power cellular metabolism. The oxidation of plastoquinol and reduction of plastocyanin by cytochrome b₆f (Cyt b₆f) is known as one of the key steps of photosynthesis, but the catalytic mechanism in the plastoquinone oxidation site (Q_p) remains elusive. Here, we describe two high-resolution cryo-EM structures of the spinach Cyt b₆f homodimer with endogenous plastoquinones and in complex with plastocyanin. Three plastoquinones are visible and line up one after another head to tail near Q_p in both monomers, indicating the existence of a channel in each monomer. Therefore, quinones appear to flow through Cyt b₆f in one direction, transiently exposing the redox-active ring of quinone during catalysis. Our work proposes an unprecedented one-way traffic model that explains efficient quinol oxidation during photosynthesis and respiration.

Electrophoretic Mobility Shift Assay (EMSA) and Microscale Thermophoresis (MST) Methods to Measure Interactions Between tRNAs and Their Modifying Enzymes

The Elongator complex is a unique tRNA acetyltransferase; it was initially annotated as a protein acetyltransferase, but in-depth biochemical analyses revealed its genuine function as a tRNA modifier. The substrate recognition and binding of the Elongator is mainly mediated by its catalytic Elp3 subunit. In this chapter, we describe protocols to generate fluorescently labeled RNAs and outline the principles underlying electrophoretic mobility shift assays (EMSA) and microscale thermophoresis (MST). These two methods allow qualitative and quantitative examinations of the binding affinity of various tRNAs toward the homologs of Elp3 from various organisms. The rather qualitative results from EMSA analyses can be nicely complemented by MST measurements allowing precise determination of the dissociation constant (K_D). We also provide detailed notes for users to mitigate potential ambiguities and technical pitfalls during the procedures.

First report of the apparent metabolisable energy value of black soldier fly larvae fat used in broiler chicken diets

In the available literature, there are limited data about the energetic value of insect-derived products. In particular, insect fat cannot be used in practical broiler nutrition due to the lack of precise apparent metabolisable energy (AME) value. Therefore, the present study aimed to investigate the AME and apparent metabolisable energy corrected to zero nitrogen balance (AME_N) levels of Hermetia illucens larvae fat for broiler chickens of various ages. A total of 400 1-day-old male Ross 308 chicks were randomly allotted to four dietary groups (10 replicate pens per treatment; 10 birds per pen). The following treatments were applied: HI0 - basal diet without dietary fat inclusion, HI03 - basal diet enriched with 30 g/kg H. illucens larvae fat, HI06 - basal diet enriched with 60 g/kg H. illucens larvae fat, and HI09 - basal diet enriched with 90 g/kg H. illucens larvae fat. Broilers had ad libitum access to mash form feed and water. Excreta samples were collected on d 14, d 28, and d 35. To determine the AME and AME_N values of H. illucens larvae fat, the simple linear regression method was used. The results show that the AME and AME_N values of H. illucens larvae fat for broiler chickens are 9 049 kcal/kg (37.86 MJ/kg) and 9 019 kcal/kg (37.74 MJ/kg), respectively. Additionally, because the birds' age significantly (P < 0.001) affected the AME and AME_N levels, the implementation of H. illucens larvae fat to broiler diets should be considered in each nutritional period using the recommended regression model AME = 2 559.758 + 62.989 × fat inclusion (%) + 7.405 × day of age and AME_N = 2 543.2663 + 62.8649 × fat inclusion (%) + 7.3777 × day of age. The present data emphasised that the H. illucens larvae fat metabolisable energy is similar to that of soybean oil.

Functional divergence of the two Elongator subcomplexes during neurodevelopment

The highly conserved Elongator complex is a translational regulator that plays a critical role in neurodevelopment, neurological diseases, and brain tumors. Numerous clinically relevant variants have been reported in the catalytic Elp123 subcomplex, while no missense mutations in the accessory subcomplex Elp456 have been described. Here, we identify ELP4 and ELP6 variants in patients with developmental delay, epilepsy, intellectual disability, and motor dysfunction. We determine the structures of human and murine Elp456 subcomplexes and locate the mutated residues. We show that patient‐derived mutations in Elp456 affect the tRNA modification activity of Elongator in vitro as well as in human and murine cells. Modeling the pathogenic variants in mice recapitulates the clinical features of the patients and reveals neuropathology that differs from the one caused by previously characterized Elp123 mutations. Our study demonstrates a direct correlation between Elp4 and Elp6 mutations, reduced Elongator activity, and neurological defects. Foremost, our data indicate previously unrecognized differences of the Elp123 and Elp456 subcomplexes for individual tRNA species, in different cell types and in different key steps during the neurodevelopment of higher organisms.

Structural basis of transposon end recognition explains central features of Tn7 transposition systems

Tn7 is a bacterial transposon with relatives containing element-encoded CRISPR-Cas systems mediating RNA-guided transposon insertion. Here, we present the 2.7 Å cryoelectron microscopy structure of prototypic Tn7 transposase TnsB interacting with the transposon end DNA. When TnsB interacts across repeating binding sites, it adopts a beads-on-a-string architecture, where the DNA-binding and catalytic domains are arranged in a tiled and intertwined fashion. The DNA-binding domains form few base-specific contacts leading to a binding preference that requires multiple weakly conserved sites at the appropriate spacing to achieve DNA sequence specificity. TnsB binding imparts differences in the global structure of the protein-bound DNA ends dictated by the spacing or overlap of binding sites explaining functional differences in the left and right ends of the element. We propose a model of the strand-transfer complex in which the terminal TnsB molecule is rearranged so that its catalytic domain is in a position conducive to transposition.

Replacement of soybean oil by Hermetia illucens fat in turkey nutrition: effect on performance, digestibility, microbial community, immune and physiological status and final product quality

1. The aim of the present study was to investigate the effect of partial (50%) or total replacement of soybean oil (SO) by black soldier fly larvae (BSFL) fat on the growth performance, coefficients of apparent nutrient digestibility, selected internal organ weights and length, pancreatic enzyme activity and gastrointestinal tract (GIT) microecology modulation, as well as microbiota activity, physiological and immunological responses in young turkey poults. 2. A total of 216, seven day old female turkeys (B.U.T 6) were randomly distributed to three dietary treatments using six replicate pens per group with 12 birds per pen. The following design of the trial was applied: SO 100% soybean oil; BSFL50 a 50/50 combination of SO and BSFL fat; or 100% BSFL fat (total replacement of SO). 3. The use of BSFL fat did not affect the growth performance, nutrient digestibility, GIT morphology, or quality of the breast and thigh muscles. However, reduced trypsin activity was noticed in the BSFL100 group, but this had no effect on digestibility. Total replacement of SO reduced proliferation of potentially pathogenic bacteria, i.e., Enterobacteriaceae spp., as well as decreasing levels of IL-6, while partial substitution lowered the TNF-α concentration. 4. The replacement of commonly used SO by BSFL fat can be successfully applied in young turkey poult nutrition. BSFL fat may be considered an antimicrobial agent and support immune responses.

Tenebrio molitor and Zophobas morio full-fat meals as functional feed additives affect broiler chickens' growth performance and immune system traits

This study was conducted to investigate the effect of insect full-fat meals (Tenebrio molitor and Zophobas morio larvae), added "on top" of a complete diet or calculated into diets, on the growth performance, selected blood, and immune system traits of broiler chickens. 1,000 one-day-old female Ross 308 broiler chicks were used in 2 independent experiments. In the first trial, the birds were randomly assigned to 6 treatments, 10 replicate pens per treatment, and 10 birds per pen, i.e., negative control; positive control with salinomycin addition (60 mg/kg diet), and addition of 0.2% and 0.3% of T. molitor and Z. morio full-fat meals "on top". In the second experiment, 4 treatments, 10 replicate pens per treatment, and 10 birds per pen were set, i.e., negative control, positive control with salinomycin addition (60 mg/kg diet), and 0.3% of T. molitor and Z. morio full-fat meals calculated in the diets. In both trials the supplementation of insects increased the BWG (Exp. 1: P = 0.024; Exp. 2: P = 0.046) and FI (Exp. 1: P = 0.022; Exp. 2: P = 0.026), and no negative effect on the FCR was recorded in experiment one (P = 0.514), however in second trial insects addition increased FCR values (P = 0.011). In addition, in the first trial, groups fed insects and PC comparing to NC decreased the IgY (P = 0.045) and IgM, (P < 0.001) levels. In the second experiment, IgM levels were also decreased (P < 0.001) in groups fed insects comparing to NC. Moreover, in first trial the IgM levels were negatively correlated to the BWG (r = -0.4845) and FI (r = -0.4986), with statistically significant values (P < 0.001). In conclusion, the current results confirmed that small amount addition (0.2% and 0.3%) of T. molitor and Z. morio full-fat meals to the diet of broiler chickens can improve growth performance and change selected the immune system traits.

The physiological response of broiler chickens to the dietary supplementation of the bacteriocin nisin and ionophore coccidiostats

The aim of this study was to investigate the effect of dietary supplementation with nisin alone or in combination with salinomycin or monensin on broiler chickens in terms of growth performance, selected blood parameters, digestive enzyme activity, apparent nutrient digestibility, and tibiotarsus mineralization, as well as selected gastrointestinal tract (GIT) organ weights, intestinal length, and central immune organ weights. Two independent experiments, each including 400 one-day-old female Ross 308 chicks differing in ionophore coccidiostats, i.e., salinomycin and monensin supplementation, were conducted. The following treatments were applied: experiment 1: NA-no additives, SAL-salinomycin (60 mg/kg diet), NIS-nisin (2,700 IU/kg diet), SAL+NIS-salinomycin (60 mg/kg diet) and nisin (2,700 IU/kg diet); experiment 2: NA-no additives, MON-monensin (100 mg/kg diet), NIS-nisin (2,700 IU/kg diet) and MON+NIS-monensin (100 mg/kg diet) and nisin (2,700 IU/kg diet). The addition of nisin with or without ionophores to the birds' diet improved broiler growth performance in terms of BWG and FCR (days 1 to 14) and BWG and FI (15 to 35 d; 1 to 35 d). Salinomycin showed effects similar to those of nisin influence on growth performance (1 to 35 d), while monensin supplementation resulted in lower BWG. Moreover, no additive effect between nisin and ionophores was observed. Nisin and salinomycin had no influence on the serum concentration of selected hormones and other blood biochemical parameters except glucose, which was reduced by nisin. A decrease in lipase activity was observed during nisin and salinomycin supplementation, while the apparent ileal digestibility of fat was not affected. However, the digestibility of crude protein increased with nisin administration. Additionally, the effects of nisin on decreasing the weight and length of GIT segments were observed. Supplementation with nisin and monensin was not associated with a negative impact on tibiotarsus mineralization and the immune organ index. This study suggests that nisin may be used in broiler nutrition as a growth promotor, with no negative influence on the bird's metabolism or immune status.

Antimycobacterial action of a new glycolipid-peptide complex obtained from extracellular metabolites of Raoultella ornithinolytica

In this paper, an antimycobacterial component of extracellular metabolites of a gut bacterium Raoultella ornithinolytica from D. veneta earthworms was isolated and its antimycobacterial action was tested using Mycobacterium smegmatis. After incubation with the complex obtained, formation of pores and furrows in cell walls was observed using microscopic techniques. The cells lost their shape, stuck together and formed clusters. Surface-enhanced Raman spectroscopy analysis showed that, after incubation, the complex was attached to the cell walls of the Mycobacterium. Analyses of the component performed with Fourier transform infrared spectroscopy demonstrated high similarity to a bacteriocin nisin, but energy dispersive X-ray spectroscopy analysis revealed differences in the elemental composition of this antimicrobial peptide. The component with antimycobacterial activity was identified using mass spectrometry techniques as a glycolipid-peptide complex. As it exhibits no cytotoxicity on normal human fibroblasts, the glycolipid-peptide complex appears to be a promising compound for investigations of its activity against pathogenic mycobacteria.

Comparative anatomy of floral elaiophores in Vitekorchis Romowicz & Szlach., Cyrtochilum Kunth and a florally dimorphic species of Oncidium Sw. (Orchidaceae: Oncidiinae)

BACKGROUND AND AIMS

Recently, molecular approaches have been used to investigate the phylogeny of subtribe Oncidiinae, resulting in the re-alignment of several of its genera. Here, a description is given of the structure of the floral elaiophores (oil glands) of four species formerly assigned to Oncidium Sw. Those of Vitekorchis excavata (Lindl.) Romowicz & Szlach., Cyrtochilum meirax (Rchb.f.) Dalström and a species of Oncidium displaying floral dimorphism, namely O. heteranthum Poepp. & Endl. var. album, are compared with that of Gomesa longipes (Lindl.) M.W. Chase & N.H. Williams, whose epithelial elaiophores are typical of many Oncidiinae, in order to extend our understanding of elaiophore diversity within this subtribe.

METHODS

Floral elaiophore structure was examined and compared at anthesis for all four species using light microscopy, scanning electron microscopy, transmission electron microscopy and histochemistry.

KEY RESULTS

In all species investigated, with the exception of C. meirax, the floral elaiophore occurs on the labellar callus and is of the intermediate type, possessing both glabrous and trichomatous regions. By contrast, although all four species produce lipid secretions, C. meirax lacks an obvious elaiophore. In each case, the secretory tissue is represented by a single-layered epidermis of cuboidal cells (trichomatous and/or atrichomatous). Palisade cells are absent. The secretion may be wax- or oil-like and is usually produced by smooth endoplasmic reticulum (SER). However, in C. meirax, where rough endoplasmic reticulum (RER) predominates, oil accumulates as plastoglobuli within elaioplasts. These plastoglobuli are then discharged into the cytoplasm, forming oil bodies. In some species, oil usually accumulates within vesicles at the plasmalemma or in the periplasmic space before traversing the cell wall and accumulating beneath the cuticle, sometimes with distension of the latter. Gomesa longipes is unusual in its production of a heterogeneous secretion, whereas Vitekorchis excavata is equally remarkable for the protuberances found on the walls of its secretory cells.

CONCLUSIONS

Anatomically, the secretory tissues of all four species, despite currently being assigned to four different genera, are remarkably similar and indicative of homoplasy. This supports previous investigations of the floral elaiophore in Oncidiinae, which showed that the same elaiophore characters may be shared by different clades, but not always by species of the same genus. Consequently, elaiophores are considered to be of limited value in investigating the phylogeny of this subtribe. Furthermore, floral dimorphism does not greatly modify elaiophore structure in the fertile flowers of Oncidium heteranthum var. album. Based on the presence or absence of well-defined elaiophores, the nature of the secretion and the cell ultrastructure, it is likely that floral oil may be produced in Oncidiinae in one of two ways: by the ER (mainly SER) or by plastids, most notably elaioplasts. Once the oil is discharged into the cytoplasm as oil bodies or oil droplets, there is little difference between the subsequent stages of oil secretion; the oil traversing the cytoplasm (often vesicle-mediated) and cell wall before accumulating beneath the cuticle.

Dietary divercin modifies gastrointestinal microbiota and improves growth performance in broiler chickens

1. The aim of the present study was to investigate the effects of dietary administration of a divercin AS7 liquid preparation on broiler chicken performance, nutrient digestibility, counts of lactic acid bacteria (LAB) and coliform bacteria, as well as on the microbial activity in the gastrointestinal tract (GIT) as expressed by digesta pH and concentrations of short-chain fatty acids and lactic acid. 2. A total of 450 1-d-old male Ross 308 chickens were randomly distributed to three dietary treatments, with 15 pens per treatment and 10 birds per pen. The dietary treatments consisted of a positive control (PC) supplemented with 60 mg/kg salinomycin, a negative control (NC) without any additives, and the divercin (DIV) supplemented diet containing 0 x 2 mL/kg of the liquid divercin AS7 preparation. 3. The dietary divercin AS7 supplementation significantly increased body weight gain at 35 d compared to the NC group. Moreover, the pH of crop contents was higher and that of caecal contents lower in birds fed on the divercin supplemented diets. 4. Significantly lower counts of LAB were observed in the crops and caeca of the birds treated with divercin. Further, the divercin supplementation decreased lactic and succinic acid concentrations in the crop and ileum. 5. The present study demonstrates that the use of divercin supplemented diets can influence composition and activity of the microbiota in the broiler chicken GIT even in the lower parts that should otherwise not be targeted due to the peptide structure of the bacteriocin.