Trichothecene Biosynthesis in Fusarium sporotrichioides: Origin of the Oxygen Atoms of T-2 Toxin

Mass spectral analysis of T-2 toxin formed during the growth of Fusarium sporotrichioides (ATCC 24043) in the presence of H₂¹⁸O showed incorporation of up to three ¹⁸O atoms per toxin molecule. The carbonyl oxygens of the acetates at C-4 and C-15 and of the isovalerate at C-8 were derived from H₂O. Toxin formed in the presence of ¹⁸O molecular oxygen incorporated up to six ¹⁸O atoms per toxin molecule. The overall incorporation was 78 and 92% of toxin molecules labeled for H₂¹⁸O and ¹⁸O₂ labeled samples, respectively. The oxygens of position 1, the 12,13-epoxide, and the hydroxyl groups at C-3, C-4, C-8, and C-15 were all derived from molecular oxygen.     

Single Atoms and Clusters Based Nanomaterials for Hydrogen Evolution,Oxygen Evolution Reactions,and Full Water Splitting

The sustainable and scalable production of hydrogen through hydrogen evolution reaction (HER) and oxygen through oxygen evolution reaction (OER) in water splitting demands efficient and robust electrocatalysts. Currently, state‐of‐the‐art electrocatalysts of Pt and IrO₂/RuO₂ exhibit the benchmark catalytic activity toward HER and OER, respectively. However, expanding their practical application is hindered by their exorbitant price and scarcity. Therefore, the development of alternative effective electrocatalysts for water splitting is crucial. In the last few decades, substantial effort has been devoted to the development of alternative HER/OER and water splitting catalysts based on various transition metals (including Fe, Co, Ni, Mo, and atomic Pt) which show promising catalytic activities and durability. In this review, after a brief introduction and basic mechanism of HER/OER, the authors systematically discuss the recent progress in design, synthesis, and application of single atom and cluster‐based HER/OER and water splitting catalysts. Moreover, the crucial factors that can tune the activity of catalysts toward HER/OER and water splitting such as morphology, crystal defects, hybridization of metals with nonmetals, heteroatom doping, alloying, and formation of metals inside graphitic layered materials are discussed. Finally, the existing challenges and future perspectives for improving the performance of electrocatalysts for water splitting are addressed.     

The Phylogenomic Roots of Modern Biochemistry: Origins of Proteins, Cofactors and Protein Biosynthesis

The complexity of modern biochemistry developed gradually on early Earth as new molecules and structures populated the emerging cellular systems. Here, we generate a historical account of the gradual discovery of primordial proteins, cofactors, and molecular functions using phylogenomic information in the sequence of 420 genomes. We focus on structural and functional annotations of the 54 most ancient protein domains. We show how primordial functions are linked to folded structures and how their interaction with cofactors expanded the functional repertoire. We also reveal protocell membranes played a crucial role in early protein evolution and show translation started with RNA and thioester cofactor-mediated aminoacylation. Our findings allow elaboration of an evolutionary model of early biochemistry that is firmly grounded in phylogenomic information and biochemical, biophysical, and structural knowledge. The model describes how primordial α-helical bundles stabilized membranes, how these were decorated by layered arrangements of β-sheets and α-helices, and how these arrangements became globular. Ancient forms of aminoacyl-tRNA synthetase (aaRS) catalytic domains and ancient non-ribosomal protein synthetase (NRPS) modules gave rise to primordial protein synthesis and the ability to generate a code for specificity in their active sites. These structures diversified producing cofactor-binding molecular switches and barrel structures. Accretion of domains and molecules gave rise to modern aaRSs, NRPS, and ribosomal ensembles, first organized around novel emerging cofactors (tRNA and carrier proteins) and then more complex cofactor structures (rRNA). The model explains how the generation of protein structures acted as scaffold for nucleic acids and resulted in crystallization of modern translation.     

Aminopropyltransferases Involved in Polyamine Biosynthesis Localize Preferentially in the Nucleus of Plant Cells

Plant aminopropyltransferases consist of a group of enzymes that transfer aminopropyl groups derived from decarboxylated S-adenosyl-methionine (dcAdoMet or dcSAM) to propylamine acceptors to produce polyamines, ubiquitous metabolites with positive charge at physiological pH. Spermidine synthase (SPDS) uses putrescine as amino acceptor to form spermidine, whereas spermine synthase (SPMS) and thermospermine synthase (TSPMS) use spermidine as acceptor to synthesize the isomers spermine and thermospermine respectively. In previous work it was shown that both SPDS1 and SPDS2 can physically interact with SPMS although no data concerning the subcellular localization was reported. Here we study the subcellular localization of these enzymes and their protein dimer complexes with gateway-based Bimolecular Fluorescence Complementation (BiFC) binary vectors. In addition, we have characterized the molecular weight of the enzyme complexes by gel filtration chromatography with in vitro assembled recombinant enzymes and with endogenous plant protein extracts. Our data suggest that aminopropyltransferases display a dual subcellular localization both in the cytosol and nuclear enriched fractions, and they assemble preferably as dimers. The BiFC transient expression data suggest that aminopropyltransferase heterodimer complexes take place preferentially inside the nucleus.     

Oxygen, the NifA gene, Nodule Structure and the Initiation of Nitrogen Fixation

Both nitrogenase and the NifA gene, which controls the expressionof the nitrogenase enzyme, require microaerobic conditions inthe infected zone of a nodule. Such conditions depend on theability of the respiratory system to consume oxygen at approximatelythe maximum rate at which it can enter that region by diffusion.The balance between consumption and supply governs the minimumsize of a functional nodule. The nature of this balance is exploredin this paper using a model. It shows that it appears physicallyimpossible for legume root nodules, below a certain minimumsize, to fix nitrogen. Furthermore, experimental data are usedto suggest that the alternative oxidase respiratory systemsmay initially provide the large respiratory capacity requiredto create microaerobic conditions, suitable for the NifA geneand nitrogenase. Nitrogen fixation, NifA gene, diffusion resistance, oxygen     

SARS-CoV-2 and the Nucleus

The ongoing COVID-19 pandemic is caused by an RNA virus, SARS-CoV-2. The genome of SARS-CoV-2 lacks a nuclear phase in its life cycle and is replicated in the cytoplasm. However, interfering with nuclear trafficking using pharmacological inhibitors greatly reduces virus infection and virus replication of other coronaviruses is blocked in enucleated cells, suggesting a critical role of the nucleus in virus infection. Here, we summarize the alternations of nuclear pathways caused by SARS-CoV-2, including nuclear translocation pathways, innate immune responses, mRNA metabolism, epigenetic mechanisms, DNA damage response, cytoskeleton regulation, and nuclear rupture. We consider how these alternations contribute to virus replication and discuss therapeutic treatments that target these pathways, focusing on small molecule drugs that are being used in clinical studies.     

Nitrogen Fixation and Hydrogen Metabolism in Cyanobacteria

Summary: This review summarizes recent aspects of (di)nitrogen fixation and (di)hydrogen metabolism, with emphasis on cyanobacteria. These organisms possess several types of the enzyme complexes catalyzing N₂ fixation and/or H₂ formation or oxidation, namely, two Mo nitrogenases, a V nitrogenase, and two hydrogenases. The two cyanobacterial Ni hydrogenases are differentiated as either uptake or bidirectional hydrogenases. The different forms of both the nitrogenases and hydrogenases are encoded by different sets of genes, and their organization on the chromosome can vary from one cyanobacterium to another. Factors regulating the expression of these genes are emerging from recent studies. New ideas on the potential physiological and ecological roles of nitrogenases and hydrogenases are presented. There is a renewed interest in exploiting cyanobacteria in solar energy conversion programs to generate H₂ as a source of combustible energy. To enhance the rates of H₂ production, the emphasis perhaps needs not to be on more efficient hydrogenases and nitrogenases or on the transfer of foreign enzymes into cyanobacteria. A likely better strategy is to exploit the use of radiant solar energy by the photosynthetic electron transport system to enhance the rates of H₂ formation and so improve the chances of utilizing cyanobacteria as a source for the generation of clean energy.     

HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures

Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer prediction lack hydrogen coordinates. We present a new algorithm, HAAD, to predict the positions of hydrogen atoms based on the positions of heavy atoms. The algorithm is built on the basic rules of orbital hybridization followed by the optimization of steric repulsion and electrostatic interactions. We tested the algorithm using three independent data sets: ultra-high-resolution X-ray structures, structures determined by neutron diffraction, and NOE proton-proton distances. Compared with the widely used programs CHARMM and REDUCE, HAAD has a significantly higher accuracy, with the average RMSD of the predicted hydrogen atoms to the X-ray and neutron diffraction structures decreased by 26% and 11%, respectively. Furthermore, hydrogen atoms placed by HAAD have more matches with the NOE restraints and fewer clashes with heavy atoms. The average CPU cost by HAAD is 18 and 8 times lower than that of CHARMM and REDUCE, respectively. The significant advantage of HAAD in both the accuracy and the speed of the hydrogen additions should make HAAD a useful tool for the detailed study of protein structure and function. Both an executable and the source code of HAAD are freely available at http://zhang.bioinformatics.ku.edu/HAAD.     

Transcriptome Analysis of Nitrogen Metabolism,Transcription Factors,and Indigoid Biosynthesis in Isatis indigotica Fort. Response to Nitrogen Availability

Journal of Plant Growth Regulation - Isatis indigotica Fort. is a popular herb in traditional Chinese medicine. It possesses pharmacological activities against various diseases, particularly...     

Antinematode Activity of Violacein and the Role of the Insulin/IGF-1 Pathway in Controlling Violacein Sensitivity in Caenorhabditis elegans

The purple pigment violacein is well known for its numerous biological activities including antibacterial, antiviral, antiprotozoan, and antitumor effects. In the current study we identify violacein as the antinematode agent produced by the marine bacterium Microbulbifer sp. D250, thereby extending the target range of this small molecule. Heterologous expression of the violacein biosynthetic pathway in E. coli and experiments using pure violacein demonstrated that this secondary metabolite facilitates bacterial accumulation in the nematode intestine, which is accompanied by tissue damage and apoptosis. Nematodes such as Caenorhabditis elegans utilise a well-defined innate immune system to defend against pathogens. Using C. elegans as a model we demonstrate the DAF-2/DAF-16 insulin/IGF-1 signalling (IIS) component of the innate immune pathway modulates sensitivity to violacein-mediated killing. Further analysis shows that resistance to violacein can occur due to a loss of DAF-2 function and/or an increased function of DAF-16 controlled genes involved in antimicrobial production (spp-1) and detoxification (sod-3). These data suggest that violacein is a novel candidate antinematode agent and that the IIS pathway is also involved in the defence against metabolites from non-pathogenic bacteria.     

植物乙烯生物合成过程中活性氧的作用

大量的研究结果表明,活性氧参与植物乙烯生物合成过程具有明显的普遍性,超氧阴离子自由基是参与乙烯生物合成过程的主要活性氧。近年来研究的焦点主要从乙烯生物合成的关键调控酶ACC合酶及ACC氧化酶的酶活性、酶动力学特性、酶蛋白空间结构、酶基因表达水平等方面来阐明活性氧调控植物乙烯生物合成的机制。最新的研究表明：植物在各种正常或应激的生长条件下首先诱导了活性氧产生水平的变化,活性氧在基因或蛋白质水平上影响ACC合酶和ACC氧化酶的活性水平,从而调节乙烯的生物合成。本文首次综述了活性氧影响植物乙烯生物合成过程的最新研究进展,并对活性氧在植物乙烯生物合成中具有诱导与抑制并存的“双重性”作用进行了探讨。     

Electrospun Carbon Nanofibers Encapsulated with NiCoP: A Multifunctional Electrode for Supercapattery and Oxygen Reduction,Oxygen Evolution,and Hydrogen Evolution Reactions

Functionalizing nanostructured carbon nanofibers (CNFs) with bimetallic phosphides enables the material to become an active electrode for multifunctional applications. A facile electrospinning technique is utilized for the first time to develop NiCoP nanoparticles encapsulated CNFs that are used as an energy storage system of supercapattery, and as an electrocatalyst for oxygen reduction, oxygen evolution, and hydrogen evolution reaction in KOH electrolyte. Evolving from the inclusion of bimetallic phosphide nanoparticles, the NiCoP/CNF electrode unveils superior‐specific capacitance (333 Fg^?1 at 2 Ag^?1) and rate capability (87%). The fabricated supercapattery device offers a voltage of 1.6 V that supplies a remarkable energy density (36 Wh kg^?1) along with an improved power density (4000 W kg^?1) and unwavering cyclic stability (25 000 cycles). Meanwhile, the NiCoP/CNF electrode has simultaneously performed well as a multifunctional electrocatalyst for oxygen reduction reaction at a half‐wave potential of 0.82 V versus reversible hydrogen electrode and can attain a current density of 10 mA cm^?2 at a very low overpotential of 268 and 130 mV for the oxygen evolution reaction and hydrogen evolution reaction, respectively. Thus, the NiCoP/CNF with all its inimitable electrode properties has profoundly proved its proficiency at handling multifunctional challenges in terms of both storage and conversion.     

Graphitic‐Shell Encapsulation of Metal Electrocatalysts for Oxygen Evolution,Oxygen Reduction,and Hydrogen Evolution in Alkaline Solution

Developing highly efficient, cost effective, and environmentally friendly electrocatalysts for the oxygen evolution reaction (OER), oxygen reduction reaction (ORR), and hydrogen evolution reaction (HER) is of interest for sustainable and clean energy technologies, including metal–air batteries and fuel cells. In this work, the screening of electrocatalytic activities of a series of single metallic iron, cobalt, and nickel nanoparticles and their binary and ternary alloys encapsulated in a graphitic carbon shell toward the OER, ORR, and HER in alkaline media is reported. Synthesis of these compounds proceeds by a two‐step sol–gel and carbothermal reduction procedure. Various ex situ characterizations show that with harsh electrochemical activation, the graphitic shell undergoes an electrochemical exfoliation. The modified electronic properties of the remaining graphene layers prevent their exfoliation, protect the bulk of the metallic cores, and participate in the electrocatalysis. The amount of near‐surface, higher‐oxidation‐state metals in the as‐prepared samples increases with electrochemical cycling, indicating that some metallic nanoparticles are not adequately encased within the graphite shell. Such surface oxide species provide secondary active sites for the electrocatalytic activities. The Ni–Fe binary system gives the most promising results for the OER, and the Co–Fe binary system shows the most promise for the ORR and HER.     

Hydrogen Production by the Thermophilic Alga Mastigocladus laminosus: Effects of Nitrogen, Temperature, and Inhibition of Photosynthesis

Hydrogen production by nitrogen-limited cultures of a thermophilic blue-green alga (cyanobacterium), Mastigocladus laminosus, was studied to develop the concept of a high-temperature biophotolysis system. Biophotolytic production of hydrogen by solar radiation was also demonstrated. Hydrogen consumption activity in these cultures was relatively high and is the present limiting factor on both the net rate and duration of hydrogen production.