Mechanism of DNA loading by the DNA repair helicase XPD

Funding: Welcome Trust Programme Grant [WT091825MA to M.F.W., J.H.N.]; Wellcome Trust [099149/Z/12/Z]; Royal Society Wolfson Merit Award (to M.F.W., J.H.N.). Funding for open access charge: Wellcome Trust [WT091825MA].The xeroderma pigmentosum group D (XPD) helicase is a component of the transcription factor IIH complex in eukaryotes and plays an essential role in DNA repair in the nucleotide excision repair pathway. XPD is a 5′ to 3′ helicase with an essential iron–sulfur cluster. Structural and biochemical studies of the monomeric archaeal XPD homologues have aided a mechanistic understanding of this important class of helicase, but several important questions remain open. In particular, the mechanism for DNA loading, which is assumed to require large protein conformational change, is not fully understood. Here, DNA binding by the archaeal XPD helicase from Thermoplasma acidophilum has been investigated using a combination of crystallography, cross-linking, modified substrates and biochemical assays. The data are consistent with an initial tight binding of ssDNA to helicase domain 2, followed by transient opening of the interface between the Arch and 4FeS domains, allowing access to a second binding site on helicase domain 1 that directs DNA through the pore. A crystal structure of XPD from Sulfolobus acidocaldiarius that lacks helicase domain 2 has an otherwise unperturbed structure, emphasizing the stability of the interface between the Arch and 4FeS domains in XPD.Publisher PDFPeer reviewe

Mechanistic insights into the plant biostimulant activity of a novel formulation based on rice husk nanobiosilica embedded in a seed coating alginate film

Seed coating ensures the targeted delivery of various compounds from the early stages of development to increase crop quality and yield. Silicon and alginate are known to have plant biostimulant effects. Rice husk (RH) is a significant source of biosilica. In this study, we coated mung bean seeds with an alginate–glycerol–sorbitol (AGS) film with embedded biogenic nanosilica (SiNPs) from RH, with significant plant biostimulant activity. After dilute acid hydrolysis of ground RH in a temperature-controlled hermetic reactor, the resulting RH substrate was neutralized and calcined at 650°C. The structural and compositional characteristics of the native RH, the intermediate substrate, and SiNPs, as well as the release of soluble Si from SiNPs, were investigated. The film for seed coating was optimized using a mixture design with three factors. The physiological properties were assessed in the absence and the presence of 50 mM salt added from the beginning. The main parameters investigated were the growth, development, metabolic activity, reactive oxygen species (ROS) metabolism, and the Si content of seedlings. The results evidenced a homogeneous AGS film formation embedding 50-nm amorphous SiNPs having Si–O–Si and Si–OH bonds, 0.347 cm3/g CPV (cumulative pore volume), and 240 m2/g SSA (specific surface area). The coating film has remarkable properties of enhancing the metabolic, proton pump activities and ROS scavenging of mung seedlings under salt stress. The study shows that the RH biogenic SiNPs can be efficiently applied, together with the optimized, beneficial alginate-based film, as plant biostimulants that alleviate saline stress from the first stages of plant development

Degradation of keratin substrates by keratinolytic fungi

Background: The hydrolysis of keratin wastes by microorganisms is considered a biotechnological alternative for recycling and valorization through keratinolytic microorganisms. Despite their resistant structure, keratin wastes can be efficiently degraded by various microorganisms through the secretion of keratinases,which are promising enzymes for several applications, including detergents, fertilizers, and leather and textile industry. In an attempt to isolate keratinolytic microorganisms that can reach commercial exploitation as keratinase producers, the current work assesses the dynamics of keratin biodegradation by several keratinolytic fungal strains isolated from soil. The activity of fungal strains to degrade keratin substrates was evaluated by SEM, FTRIR-ATR spectra and TGA analysis. Results: SEM observations offered relevant information on interactions between microorganism and structural elements of hair strands. FTIR spectra of the bands at 1035\u20131075 cm-1 assigned to sulfoxide bond appeared because of S\u2013S bond breaking, which demonstrated the initiation of keratin biodegradation. According to TGA, in the second zone of thermal denaturation, where keratin degradation occurs, the highest weight loss of 71.10% was obtained for sample incubated with Fusarium sp. 1A. Conclusions: Among the tested strains, Fusarium sp. 1A was the most active organism in the degradation process with the strongest denaturation of polypeptide chains. Because keratinolytic microorganisms and their enzymes keratinases represent a subject of scientific and economic interest because of their capability to hydrolyze keratin, Fusarium sp. 1A was selected for further studies

Selenium Analysis and Speciation in Dietary Supplements Based on Next-Generation Selenium Ingredients

Selenium is essential for humans and the deficit of Se requires supplementation. In addition to traditional forms such as Se salts, amino acids, or selenium-enriched yeast supplements, next-generation selenium supplements, with lower risk for excess supplementation, are emerging. These are based on selenium forms with lower toxicity, higher bioavailability, and controlled release, such as zerovalent selenium nanoparticles (SeNPs) and selenized polysaccharides (SPs). This article aims to focus on the existing analytical systems for the next-generation Se dietary supplement, providing, at the same time, an overview of the analytical methods available for the traditional forms. The next-generation dietary supplements are evaluated in comparison with the conventional/traditional ones, as well as the analysis and speciation methods that are suitable to reveal which Se forms and species are present in a dietary supplement. Knowledge gaps and further research potential in this field are highlighted. The review indicates that the methods of analysis of next-generation selenium supplements should include a step related to chemical species separation. Such a step would allow a proper characterization of the selenium forms/species, including molecular mass/dimension, and substantiates the marketing claims related to the main advantages of these new selenium ingredients

Closing the Nutrient Loop—The New Approaches to Recovering Biomass Minerals during the Biorefinery Processes

The recovery of plant mineral nutrients from the bio-based value chains is essential for a sustainable, circular bioeconomy, wherein resources are (re)used sustainably. The widest used approach is to recover plant nutrients on the last stage of biomass utilization processes—e.g., from ash, wastewater, or anaerobic digestate. The best approach is to recover mineral nutrients from the initial stages of biomass biorefinery, especially during biomass pre-treatments. Our paper aims to evaluate the nutrient recovery solutions from a trans-sectorial perspective, including biomass processing and the agricultural use of recovered nutrients. Several solutions integrated with the biomass pre-treatment stage, such as leaching/bioleaching, recovery from pre-treatment neoteric solvents, ionic liquids (ILs), and deep eutectic solvents (DESs) or integrated with hydrothermal treatments are discussed. Reducing mineral contents on silicon, phosphorus, and nitrogen biomass before the core biorefinery processes improves processability and yield and reduces corrosion and fouling effects. The recovered minerals are used as bio-based fertilizers or as silica-based plant biostimulants, with economic and environmental benefits

Patterns of protein stability and interactions in water-cosolvent systems

The basis of the present study represents the aim in bringing a contribution to the elucidation of certain thermodynamic and molecular aspects characterizing protein-cosolvent and protein-protein interactions and how these two types of interactions are interrelated. The investigation of protein-cosolvent systems was mainly based on ionic species and, in particular, on a special class of organic salts known under the general name of "ionic liquids". By investigating a multitude of ionic liquids, it was possible to rank them in a Hofmeister series, based on the extent of stabilizing/destabilizing effect on the proteins. More, the ionic liquids show the capacity to prevent protein aggregation. The unfolding - dissociation mechanism and the thermodynamic equilibrium between the oligomerization domains of MST1 and Nore1 (the SARAH domains) - having a role in the Ras-induced apoptosis pathway was also investigated

Taking a molecular motor for a spin : helicase mechanism studied by spin labelling and PELDOR

Welcome Trust programme grant [WT091825MA to M.F.W., J.H.N.]; Wellcome Trust multi-user equipment grant [099149/Z/12/Z]. Royal Society Wolfseon Merit Award (to M.F.W., J.H.N.). Funding for open access charge: Wellcome Trust [WT091825MA].The complex molecular motions central to the functions of helicases have long attracted attention. Protein crystallography has provided transformative insights into these dynamic conformational changes, however important questions about the true nature of helicase configurations during the catalytic cycle remain. Using pulsed EPR (PELDOR or DEER) to measure interdomain distances in solution, we have examined two representative helicases: PcrA from superfamily 1 and XPD from superfamily 2. The data show that PcrA is a dynamic structure with domain movements that correlate with particular functional states, confirming and extending the information gleaned from crystal structures and other techniques. XPD in contrast is shown to be a rigid protein with almost no conformational changes resulting from nucleotide or DNA binding, which is well described by static crystal structures. Our results highlight the complimentary nature of PELDOR to crystallography and the power of its precision in understanding the conformational changes relevant to helicase function.Publisher PDFPeer reviewe

In Silico Approach toward Analysing the Bioactive Effects of Spent Brewery Yeast Proteins

Saccharomyces cerevisiae, a yeast widely used in food and beverage production, was observed to provide a valuable source of different nutrients, the most important being the bioactive peptides which can become a major supporter in pharmaceutical therapies [...

Optimization of Chitin Extraction from Agaricus bisporus Using a Taguchi Design

Edible mushrooms, e.g., Agaricus bisporus (A. bisporus), represents. [...

Enhancement of Lignolytic Enzyme Activity in Ganoderma Lucidum by Co-Cultivation with Bacteria

Fungi are known for their capacity to produce two main categories of enzymes, cellulolytic and lignolytic, both valuable for biodegradation of lignocellulosic biomass [...