Endogenous plant nitroxyl, a new component of nitric oxide biology.

Nitroxyl (HNO), a one-electron reduced and protonated congener of nitric oxide (•NO), was recently discovered in Arabidopsis thaliana. Due to its distinct chemical properties, we believe HNO must be further studied to determine how many physiological processes it impacts.

PEP444c encoded within the MIR444c gene regulates microRNA444c accumulation in barley.

MicroRNAs are small, noncoding RNA molecules that regulate the expression of their target genes. The MIR444 gene family is present exclusively in monocotyledons, and microRNAs444 from this family have been shown to target certain MADS-box transcription factors in rice and barley. We identified three barley MIR444 (MIR444a/b/c) genes and comprehensively characterised their structure and the processing pattern of the primary transcripts (pri-miRNAs444). Pri-microRNAs444 undergo extensive alternative splicing, generating functional and nonfunctional pri-miRNA444 isoforms. We show that barley pri-miRNAs444 contain numerous open reading frames (ORFs) whose transcripts associate with ribosomes. Using specific antibodies, we provide evidence that selected ORFs encoding PEP444a within MIR444a and PEP444c within MIR444c are expressed in barley plants. Moreover, we demonstrate that CRISPR-associated endonuclease 9 (Cas9)-mediated mutagenesis of the PEP444c-encoding sequence results in a decreased level of PEP444 transcript in barley shoots and roots and a 5-fold reduced level of mature microRNA444c in roots. Our observations suggest that PEP444c encoded by the MIR444c gene is involved in microRNA444c biogenesis in barley.

Dynamics of nitration during dark-induced leaf senescence in Arabidopsis reveals proteins modified by tryptophan nitration.

Nitric oxide (NO) is a critical molecule that links plant development with stress responses. Herein, new insights into the role of NO metabolism during leaf senescence in Arabidopsis are presented. A gradual decrease in NO emission accompanied dark-induced leaf senescence (DILS), and a transient wave of peroxynitrite (ONOO-) formation was detected by day 3 of DILS. The boosted ONOO- did not promote tryptophan (Trp) nitration, while the pool of 6-nitroTrp-containing proteins was depleted as senescence progressed. Immunoprecipitation combined with mass spectrometry was used to identify 63 and 4 characteristic 6-nitroTrp-containing proteins in control and individually darkened leaves, respectively. The potential in vivo targets of Trp nitration were mainly related to protein biosynthesis and carbohydrate metabolism. In contrast, nitration of tyrosine-containing proteins was intensified 2-fold on day 3 of DILS. Also, nitrative modification of RNA and DNA increased significantly on days 3 and 7 of DILS, respectively. Taken together, ONOO- can be considered a novel pro-senescence regulator that fine-tunes the redox environment for selective bio-target nitration. Thus, DILS-triggered nitrative changes at RNA and protein levels promote developmental shifts during the plant's lifespan and temporal adjustment in plant metabolism under suboptimal environmental conditions.

Epigenetic Landmarks of Leaf Senescence and Crop Improvement.

This review synthesizes knowledge on epigenetic regulation of leaf senescence and discusses the possibility of using this knowledge to improve crop quality. This control level is implemented by different but interacting epigenetic mechanisms, including DNA methylation, covalent histone modifications, and non-covalent chromatin remodeling. The genetic and epigenetic changes may act alone or together and regulate the gene expression, which may result in heritable (stress memory) changes and may lead to crop survival. In the review, the question also arises whether the mitotically stable epigenetic information can be used for crop improvement. The barley crop model for early and late events of dark-induced leaf senescence (DILS), where the point of no return was defined, revealed differences in DNA and RNA modifications active in DILS compared to developmental leaf senescence. This suggests the possibility of a yet-to-be-discovered epigenetic-based switch between cell survival and cell death. Conclusions from the analyzed research contributed to the hypothesis that chromatin-remodeling mechanisms play a role in the control of induced leaf senescence. Understanding this mechanism in crops might provide a tool for further exploitation toward sustainable agriculture: so-called epibreeding.

Physio-Genetic Dissection of Dark-Induced Leaf Senescence and Timing Its Reversal in Barley.

Barley crop model was analyzed for early and late events during the dark-induced leaf senescence (DILS) as well as for deciphering critical time limit for reversal of the senescence process. Chlorophyll fluorescence vitality index Rfd was determined as the earliest parameter that correlated well with the cessation of photosynthesis prior to microautophagy symptoms, initiation of DNA degradation, and severalfold increase in the endonuclease BNUC1. DILS was found characterized by up-regulation of processes that enable recycling of degraded macromolecules and metabolites, including increased NH4 + remobilization, gluconeogenesis, glycolysis, and partial up-regulation of glyoxylate and tricarboxylate acid cycles. The most evident differences in gene medleys between DILS and developmental senescence included hormone-activated signaling pathways, lipid catabolic processes, carbohydrate metabolic processes, low-affinity ammonia remobilization, and RNA methylation. The mega-autophagy symptoms were apparent much later, specifically on day 10 of DILS, when disruption of organelles-nucleus and mitochondria -became evident. Also, during this latter-stage programmed cell death processes, namely, shrinking of the protoplast, tonoplast interruption, and vacuole breakdown, chromatin condensation, more DNA fragmentation, and disintegration of the cell membrane were prominent. Reversal of DILS by re-exposure of the plants from dark to light was possible until but not later than day 7 of dark exposure and was accompanied by regained photosynthesis, increase in chlorophyll, and reversal of Rfd, despite activation of macro-autophagy-related genes.

Benzyl alcohol oxidation with Pd-Zn/TiO2: computational and experimental studies.

Pd-Zn/TiO2 catalysts containing 1 wt% total metal loading, but with different Pd to Zn ratios, were prepared using a modified impregnation method and tested in the solvent-free aerobic oxidation of benzyl alcohol. The catalyst with the higher Pd content exhibited an enhanced activity for benzyl alcohol oxidation. However, the selectivity to benzaldehyde was significantly improved with increasing presence of Zn. The effect of reduction temperature on catalyst activity was investigated for the catalyst having a Pd to Zn metal molar ratio of 9:1. It was found that lower reduction temperature leads to the formation of PdZn nanoparticles with a wide particle size distribution. In contrast, smaller PdZn particles were formed upon catalyst reduction at higher temperatures. Computational studies were performed to compare the adsorption energies of benzyl alcohol and the reaction products (benzaldehyde and toluene) on PdZn surfaces to understand the oxidation mechanism and further explain the correlation between the catalyst composition and its activity.

Oxidation of Polynuclear Aromatic Hydrocarbons using Ruthenium-Ion-Catalyzed Oxidation: The Role of Aromatic Ring Number in Reaction Kinetics and Product Distribution.

Oxidation of aromatic hydrocarbons with differing numbers of fused aromatic rings (2-5), have been studied in two solvent environments (monophasic and biphasic) using ruthenium-ion-catalyzed oxidation (RICO). RICO reduces the aromaticity of the polyaromatic core of the molecule in a controlled manner by selective oxidative ring opening. Moreover, the nature of the solvent system determines the product type and distribution, for molecules with more than two aromatic rings. Competitive oxidation between substrates with different numbers of aromatic rings has been studied in detail. It was found that the rate of polyaromatic hydrocarbon oxidation increases with the number of fused aromatic rings. A similar trend was also identified for alkylated aromatic hydrocarbons. The proof-of-concept investigation provides new insight into selective oxidation chemistry for upgrading of polyaromatic molecules.

Mechanistic Insights into Selective Oxidation of Polyaromatic Compounds using RICO Chemistry.

Ruthenium-ion-catalyzed oxidation (RICO) of polyaromatic hydrocarbons (PAHs) has been studied in detail using experimental and computational approaches to explore the reaction mechanism. DFT calculations show that regioselectivity in these reactions can be understood in terms of the preservation of aromaticity in the initial formation of a [3+2] metallocycle intermediate at the most-isolated double bond. We identify two competing pathways: C-C bond cleavage leading to a dialdehyde and C-H activation followed by H migration to the RuOx complex to give diketones. Experimentally, the oxidation of pyrene and phenanthrene has been carried out in monophasic and biphasic solvent systems. Our results show that diketones are the major product for both phenanthrene and pyrene substrates. These diketone products are shown to be stable under our reaction conditions so that higher oxidation products (acids and their derivatives) are assigned to the competing pathway through the dialdehyde. Experiments using 18 O-labelled water do show incorporation of oxygen from the solvents into products, but this may take place during the formation of the reactive RuO4 species rather than directly during PAH oxidation. When the oxidation of pyrene is carried out using D2 O, a kinetic isotope effect (KIE) is observed implying that water is involved in the rate-determining step leading to the diketone products.

Activation and Deactivation of Gold/Ceria-Zirconia in the Low-Temperature Water-Gas Shift Reaction.

Gold (Au) on ceria-zirconia is one of the most active catalysts for the low-temperature water-gas shift reaction (LTS), a key stage of upgrading H2 reformate streams for fuel cells. However, this catalyst rapidly deactivates on-stream and the deactivation mechanism remains unclear. Using stop-start scanning transmission electron microscopy to follow the exact same area of the sample at different stages of the LTS reaction, as well as complementary X-ray photoelectron spectroscopy, we observed the activation and deactivation of the catalyst at various stages. During the heating of the catalyst to reaction temperature, we observed the formation of small Au nanoparticles (NPs; 1-2 nm) from subnanometer Au species. These NPs were then seen to agglomerate further over 48 h on-stream, and most rapidly in the first 5 h when the highest rate of deactivation was observed. These findings suggest that the primary deactivation process consists of the loss of active sites through the agglomeration and possible dewetting of Au NPs.

Selective oxidation of alkyl-substituted polyaromatics using ruthenium-ion-catalyzed oxidation.

Ruthenium-ion-catalyzed oxidation of a range of alkylated polyaromatics has been studied. 2-Ethylnaphthalene was used as a model substrate, and oxidation can be performed in either a conventional biphasic or in a monophasic solvent system. In either case the reaction rates and product selectivity are identical. The reaction products indicate that the aromatic ring system is oxidized in preference to the alkyl chain. This analysis is possible due to the development of a quantitative NMR protocol to determine the relative amounts of aliphatic and aromatic protons. From a systematic set of substrates we show that as the length of the alkyl chain substituent on a polyaromatic increases, the proportion of products in which the chain remains attached to the aromatic system increases. Larger polyaromatic systems, based on pyrene and phenanthrene, show greater reactivity than those with fewer aromatic rings, and the alkyl chains are more stable to oxidation.

The use of carbon monoxide as a probe molecule in spectroscopic studies for determination of exposed gold sites on TiO2.

The sol immobilisation technique, in which a stabilising ligand (such as polyvinyl alcohol or polyvinyl pyridine) can be used to tune metal particle size and composition, has become a valuable method of making supported nanoparticle catalysts. An unfortunate consequence of the stabilising ligand is that often access of reactant molecules to the metal nanoparticle surface is impeded. Several methods have been proposed for the removal of these ligands, though determination of the degree of their success is difficult. Here, we demonstrate the use of in situ infrared and UV-Vis spectroscopy to elucidate the access of carbon monoxide to the surface of Au/TiO2 catalysts before and after various ligand removal treatments. These were contrasted with a catalyst prepared by deposition precipitation prepared in the absence of stabilising ligand as a control. Changes were observed in the infrared spectrum, with the wavenumber of carbon monoxide linearly bonded to Au for catalysts shifting before and after ligand removal, which correlated well with the activity of the catalyst for carbon monoxide oxidation. Also the extent of shifting of the Au surface resonance plasmon band on the addition of carbon monoxide, observed by UV-Vis, also correlated well with catalyst activity. These simple methods can be used to determine the quantity of exposed metal sites after a ligand removal treatment and so determine the treatments effectiveness.

Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology.

Phytophthora species are oomycetes that have evolved a broad spectrum of biological processes and improved strategies to cope with host and environmental challenges. A growing body of evidence indicates that the high pathogen plasticity is based on epigenetic regulation of gene expression linked to Phytophthora's rapid adjustment to endogenous cues and various stresses. As 5mC DNA methylation has not yet been identified in Phytophthora, the reversible processes of acetylation/deacetylation of histone proteins seem to play a pivotal role in the epigenetic control of gene expression in oomycetes. To explore this issue, we review the structure, diversity, and phylogeny of histone acetyltransferases (HATs) and histone deacetylases (HDACs) in six plant-damaging Phytophthora species: P. capsici, P. cinnamomi, P. infestans, P. parasitica, P. ramorum, and P. sojae. To further integrate and improve our understanding of the phylogenetic classification, evolutionary relationship, and functional characteristics, we supplement this review with a comprehensive view of HATs and HDACs using recent genome- and proteome-level databases. Finally, the potential functional role of transcriptional reprogramming mediated by epigenetic changes during Phytophthora species saprophytic and parasitic phases under nitro-oxidative stress is also briefly discussed.

In situ spectroscopic investigation of oxidative dehydrogenation and disproportionation of benzyl alcohol.

In the solvent free oxidation of benzyl alcohol, using supported gold-palladium nanoalloys, toluene is often one of major by-products and it is formed by the disproportionation of benzyl alcohol. Gold-palladium catalysts on acidic supports promote both the disproportionation of benzyl alcohol and oxidative dehydrogenation to form benzaldehyde. Basic supports completely switch off disproportionation and the gold-palladium nanoparticles catalyse the oxidative dehydrogenation reaction exclusively. In an attempt to provide further details on the course of these reactions, we have utilized in situ ATR-IR, in situ DRIFT and inelastic neutron scattering spectroscopic methods, and in this article we present the results of these in situ spectroscopic studies.

Insight into metabolic sensors of nitrosative stress protection in Phytophthora infestans.

Phytophthora infestans, a representative of phytopathogenic oomycetes, have been proven to cope with redundant sources of internal and host-derived reactive nitrogen species (RNS). To gain insight into its nitrosative stress resistance mechanisms, metabolic sensors activated in response to nitrosative challenge during both in vitro growth and colonization of the host plant were investigated. The conducted analyses of gene expression, protein accumulation, and enzyme activity reveal for the first time that P. infestans (avirulent MP946 and virulent MP977 toward potato cv. Sarpo Mira) withstands nitrosative challenge and has an efficient system of RNS elimination. The obtained data indicate that the system protecting P. infestans against nitric oxide (NO) involved the expression of the nitric oxide dioxygenase (Pi-NOD1) gene belonging to the globin family. The maintenance of RNS homeostasis was also supported by an elevated S-nitrosoglutathione reductase activity and upregulation of peroxiredoxin 2 at the transcript and protein levels; however, the virulence pattern determined the expression abundance. Based on the experiments, it can be concluded that P. infestans possesses a multifarious system of metabolic sensors controlling RNS balance via detoxification, allowing the oomycete to exist in different micro-environments flexibly.

Metal tolerance gene family in barley: an in silico comprehensive analysis.

Metal-tolerance proteins (MTPs) are divalent cation transporters that play critical roles in metal tolerance and ion homeostasis in plants. However, a comprehensive study of MTPs is still lacking in crop plants. The current study aimed to comprehensively identify and characterize the MTP gene family in barley (Hordeum vulgare, Hv), an important crop. In total, 12 HvMTPs were identified in the barley genome in this study. They were divided into three phylogenetic groups (Zn-cation diffusion facilitator proteins [CDFs], Fe/Zn-CDFs, and Mn-CDFs) and further subdivided into seven groups (G1, G5, G6, G7, G8, G9, and G12). The majority of MTPs were hydrophobic proteins found in the vacuolar membrane. Gene duplication analysis of HvMTPs revealed one pair of segmental-like duplications in the barley genome. Evolutionary analysis suggested that barley MTPs underwent purifying natural selection. Additionally, the HvMTPs were analyzed in the pan-genome sequences of barley (20 accessions), which suggests that HvMTPs are highly conserved in barley evolution. Cis-acting regulatory elements, microRNA target sites, and protein-protein interaction analysis indicated the role of HvMTPs in a variety of biological processes. Expression profiling suggests that HvMTPs play an active role in maintaining barley nutrient homeostasis throughout its life cycle, and their expression levels were not significantly altered by abiotic stresses like cold, drought, or heat. The expression of barley HvMTP genes in the presence of heavy metals such as Zn2+, Cu2+, As3+, and Cd2+ revealed that these MTPs were induced by at least one metal ion, implying their involvement in metal tolerance or transportation. The identification and comprehensive investigation of MTP gene family members will provide important gene resources for the genetic improvement of crops for metal tolerance, bioremediation, or biofortification of staple crops.

Genetic portrait of polyamine transporters in barley: insights in the regulation of leaf senescence.

Nitrogen (N) is one of the most expensive nutrients to supply, therefore, improving the efficiency of N use is essential to reduce the cost of commercial fertilization in plant production. Since cells cannot store reduced N as NH3 or NH4 +, polyamines (PAs), the low molecular weight aliphatic nitrogenous bases, are important N storage compounds in plants. Manipulating polyamines may provide a method to increase nitrogen remobilization efficiency. Homeostasis of PAs is maintained by intricate multiple feedback mechanisms at the level of biosynthesis, catabolism, efflux, and uptake. The molecular characterization of the PA uptake transporter (PUT) in most crop plants remains largely unknown, and knowledge of polyamine exporters in plants is lacking. Bi-directional amino acid transporters (BATs) have been recently suggested as possible PAs exporters for Arabidopsis and rice, however, detailed characterization of these genes in crops is missing. This report describes the first systematic study to comprehensively analyze PA transporters in barley (Hordeum vulgare, Hv), specifically the PUT and BAT gene families. Here, seven PUTs (HvPUT1-7) and six BATs (HvBAT1-6) genes were identified as PA transporters in the barley genome and the detailed characterization of these HvPUT and HvBAT genes and proteins is provided. Homology modeling of all studied PA transporters provided 3D structures prediction of the proteins of interest with high accuracy. Moreover, molecular docking studies provided insights into the PA-binding pockets of HvPUTs and HvBATs facilitating improved understanding of the mechanisms and interactions involved in HvPUT/HvBAT-mediated transport of PAs. We also examined the physiochemical characteristics of PA transporters and discuss the function of PA transporters in barley development, and how they help barley respond to stress, with a particular emphasis on leaf senescence. Insights gained here could lead to improved barley production via modulation of polyamine homeostasis.

Plant Transglutaminases: New Insights in Biochemistry, Genetics, and Physiology.

Transglutaminases (TGases) are calcium-dependent enzymes that catalyse an acyl-transfer reaction between primary amino groups and protein-bound Gln residues. They are widely distributed in nature, being found in vertebrates, invertebrates, microorganisms, and plants. TGases and their functionality have been less studied in plants than humans and animals. TGases are distributed in all plant organs, such as leaves, tubers, roots, flowers, buds, pollen, and various cell compartments, including chloroplasts, the cytoplasm, and the cell wall. Recent molecular, physiological, and biochemical evidence pointing to the role of TGases in plant biology and the mechanisms in which they are involved allows us to consider their role in processes such as photosynthesis, plant fertilisation, responses to biotic and abiotic stresses, and leaf senescence. In the present paper, an in-depth description of the biochemical characteristics and a bioinformatics comparison of plant TGases is provided. We also present the phylogenetic relationship, gene structure, and sequence alignment of TGase proteins in various plant species, not described elsewhere. Currently, our knowledge of these proteins in plants is still insufficient. Further research with the aim of identifying and describing the regulatory components of these enzymes and the processes regulated by them is needed.

Fungal and oomycete pathogens and heavy metals: an inglorious couple in the environment.

Heavy metal (HM) contamination of the environment is a major problem worldwide. The rate of global deposition of HMs in soil has dramatically increased over the past two centuries and there of facilitated their rapid accumulation also in living systems. Although the effects of HMs on plants, animals and humans have been extensively studied, yet little is known about their effects on the (patho)biology of the microorganisms belonging to a unique group of filamentous eukaryotic pathogens, i.e., fungi and oomycetes. Much of the literature concerning mainly model species has revealed that HM stress affects their hyphal growth, morphology, and sporulation. Toxicity at cellular level leads to disturbance of redox homeostasis manifested by the formation of nitro-oxidative intermediates and to the induction of antioxidant machinery. Despite such adverse effects, published data is indicative of the fact that fungal and oomycete pathogens have a relatively high tolerance to HMs in comparison to other groups of microbes such as bacteria. Likely, these pathogens may harbor a network of detoxification mechanisms that ensure their survival in a highly HM-polluted (micro)habitat. Such a network may include extracellular HMs immobilization, biosorption to cell wall, and/or their intracellular sequestration to proteins or other ligands. HMs may also induce a hormesis-like phenomenon allowing the pathogens to maintain or even increase fitness against chemical challenges. Different scenarios linking HMs stress and modification of the microorganisms pathogenicity are disscused in this review.

Comparative genomic analysis of the aldehyde dehydrogenase gene superfamily in Arabidopsis thaliana - searching for the functional key to hypoxia tolerance.

Flooding entails different stressful conditions leading to low oxygen availability for respiration and as a result plants experience hypoxia. Stress imposed by hypoxia affects cellular metabolism, including the formation of toxic metabolites that dramatically reduce crop productivity. Aldehyde dehydrogenases (ALDHs) are a group of enzymes participating in various aspects of plant growth, development and stress responses. Although we have knowledge concerning the multiple functionalities of ALDHs in tolerance to various stresses, the engagement of ALDH in plant metabolism adjustment to hypoxia is poorly recognized. Therefore, we explored the ALDH gene superfamily in the model plant Arabidopsis thaliana. Genome-wide analyses revealed that 16 AtALDH genes are organized into ten families and distributed irregularly across Arabidopsis 5 chromosomes. According to evolutionary relationship studies from different plant species, the ALDH gene superfamily is highly conserved. AtALDH2 and ALDH3 are the most numerous families in plants, while ALDH18 was found to be the most distantly related. The analysis of cis-acting elements in promoters of AtALDHs indicated that AtALDHs participate in responses to light, phytohormones and abiotic stresses. Expression profile analysis derived from qRT-PCR showed the AtALDH2B7, AtALDH3H1 and AtALDH5F1 genes as the most responsive to hypoxia stress. In addition, the expression of AtALDH18B1, AtALDH18B2, AtALDH2B4, and AtALDH10A8 was highly altered during the post-hypoxia-reoxygenation phase. Taken together, we provide comprehensive functional information on the ALDH gene superfamily in Arabidopsis during hypoxia stress and highlight ALDHs as a functional element of hypoxic systemic responses. These findings might help develop a framework for application in the genetic improvement of crop plants.

N6-methyladenosine (m6A) RNA modification as a metabolic switch between plant cell survival and death in leaf senescence.

Crop losses caused by climate change and various (a)biotic stressors negatively affect agriculture and crop production. Therefore, it is vital to develop a proper understanding of the complex response(s) to (a)biotic stresses and delineate them for each crop plant as a means to enable translational research. In plants, the improvement of crop quality by m6A editing is believed to be a promising strategy. As a reaction to environmental changes, m6A modification showed a high degree of sensitivity and complexity. We investigated differences in gene medleys between dark-induced leaf senescence (DILS) and developmental leaf senescence in barley, including inter alia RNA modifications active in DILS. The identified upregulated genes in DILS include RNA methyltransferases of different RNA types, embracing enzymes modifying mRNA, tRNA, and rRNA. We have defined a decisive moment in the DILS model which determines the point of no return, but the mechanism of its control is yet to be uncovered. This indicates the possibility of an unknown additional switch between cell survival and cell death. Discoveries of m6A RNA modification changes in certain RNA species in different stages of leaf senescence may uncover the role of such modifications in metabolic reprogramming. Nonetheless, there is no such data about the process of leaf senescence in plants. In this scope, the prospect of finding connections between the process of senescence and m6A modification of RNA in plants seems to be compelling.