Variable oxygen environments and DNMT2 determine the DNA cytosine epigenetic landscape of Plasmodium falciparum

DNA cytosine methylation and its oxidized products are important epigenetic modifications in mammalian cells. Although 5-methylcytosine (5mC) was detected in the human malaria parasite Plasmodium falciparum, the presence of oxidized 5mC forms remain to be characterized.Here we establish a protocol to explore nuclease-based DNA digestion for the extremely AT-rich genome of P. falciparum (>80% A+T) for quantitative LC-MS/MS analysis of 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). We demonstrate the presence of 5hmC, 5fC and 5caC cytosine modifications in a DNMT2-only organism and observe striking ratio changes between 5mC and 5hmC during the 48-hour blood stage parasite development. Parasite-infected red blood cells cultured in different physiological oxygen concentrations revealed a shift in the cytosine modifications distribution towards the oxidized 5hmC and 5caC forms. In the absence of the canonical C5-DNA methyltransferase (DNMT1 and DNMT3A/B) in P. falciparum, we show that all cytosine modifications depend on the presence of DNMT2. We conclude that DNMT2 and oxygen levels are critical determinants that shape the dynamic cytosine epigenetic landscape in this human pathogen.

Primary Phosphines and Phosphine Oxides with a Stereogenic Carbon Center Adjacent to the Phosphorus Atom: Synthesis and Anti-Markovnikov Radical Addition to Alkenes

Organophosphorus compounds with stereogenic phosphorus and carbon atoms have received increasing attention. In this regards, primary phosphines with a stereogenic carbon atom adjacent to the phosphorus atom were synthesized by the reduction in phosphonates and phosphonoselenoates with a binaphthyl group. Their oxidized products, i.e., phosphine oxides with a stereogenic tetrasubstituted carbon atom, were found to undergo BEt3-mediated radical addition to cyclohexene to give P-stereogenic secondary phosphine oxides with a diastereoselectivity of 91:9. The products were characterized by ordinary analytical methods, such as Fourier transform infrared spectroscopy; 1H, 13C, and 31P NMR spectroscopies; and mass spectroscopy. Computational studies on the phosphorus-centered radical species and the obtained product implied that the thermodynamically stable radical and the adduct may be formed as a major diastereomer. The radical addition to a range of alkenes took place in an anti-Markovnikov fashion to give P-stereogenic secondary phosphine oxides. A variety of functional groups in the alkenes were tolerated under the reaction conditions to afford secondary phosphine oxides in moderate yields. Primary phosphines with an alkenyl group, which were generated in situ, underwent intramolecular cyclization to give five- and six-membered cyclic phosphines in high yields after protection by BH3.

Quantifying oxidation of cellulose-associated glucuronoxylan by two lytic polysaccharide monooxygenases from Neurospora crassa

Family AA9 lytic polysaccharide monooxygenases (LPMOs) are abundant in fungi where they catalyze oxidative depolymerization of recalcitrant plant biomass. These AA9 LPMOs cleave cellulose, and some also act on hemicelluloses, primarily other (substituted) β-(1→4)-glucans. Oxidative cleavage of xylan has been shown for only a handful AA9 LPMOs, and it remains unclear whether this activity is a minor side reaction or primary function. Here, we show that Nc LPMO9F and the phylogenetically related, hitherto uncharacterized Nc LPMO9L from Neurospora crassa are active on both cellulose and cellulose-associated glucuronoxylan, but not on glucuronoxylan alone. A newly developed method for simultaneous quantification of xylan-derived and cellulose-derived oxidized products showed that Nc LPMO9F preferentially cleaves xylan when acting on a cellulose–beechwood glucuronoxylan mixture, yielding about three times more xylan-derived than cellulose-derived oxidized products. Interestingly, under similar conditions, Nc LPMO9L and previously characterized Mc LPMO9H from Malbranchea cinnamomea showed different xylan-to-cellulose preferences, giving oxidized product ratios of about 0.5:1 and 1:1, respectively, indicative of functional variation among xylan-active LPMOs. Phylogenetic and structural analysis of xylan-active AA9 LPMOs led to the identification of characteristic structural features, including unique features that do not occur in phylogenetically remote AA9 LPMOs, such as four AA9 LPMOs whose lack of activity towards glucuronoxylan was demonstrated in the present study. Taken together, the results provide a path towards discovery of additional xylan-active LPMOs and show that the huge family of AA9 LPMOs has members that preferentially act on xylan. These findings shed new light on the biological role and industrial potential of these fascinating enzymes. Importance Plant cell wall polysaccharides are highly resilient to depolymerization by hydrolytic enzymes, partly due to cellulose chains being tightly packed in microfibrils that are covered by hemicelluloses. Lytic polysaccharide monooxygenases (LPMOs) seem well suited to attack these resilient co-polymeric structures, but the occurrence and importance of hemicellulolytic activity among LPMOs remains unclear. Here we show that certain AA9 LPMOs preferentially cleave xylan when acting on a cellulose–glucuronoxylan mixture, and that this ability is the result of protein evolution that has resulted in a clade of AA9 LPMOs with specific structural features. Our findings strengthen the notion that the vast arsenal of AA9 LPMOs in certain fungal species provides functional versatility, and that AA9 LPMOs may have evolved to promote oxidative depolymerization of a wide variety of recalcitrant, co-polymeric plant polysaccharide structures. These findings have implications for understanding the biological roles and industrial potential of LPMOs.

Enzymatic transformation products of phloretin as potent anti-adipogenic compounds

Enzymatic structure modification of the representative chalcone phloretin (1) with polyphenol oxidase from Agaricus bisporus origin produced two new biphenyl-type phloreoxin (2) and phloreoxinone (3), and a previously undescribed (2R)-5,7,3“,5”-tetrahydroxyflavanone (4). The structure of these new oxidized products 2‒4 elucidated by interpreting the spectroscopic data (NMR and FABMS) containing the absolute stereochemistry established by analysis of the circular dichroism (CD) spectrum. Compared to the original phloretin, the new products (2) and (3) showed highly improved anti-adipogenic potencies both toward pancreatic lipase and accumulation of 3T3-L1 cells. Aslo, phloreoxin (2) effectively inhibited the expression of C/EBPβ, PPARγ, and aP2 at the mRNA level in the 3T3 adipocytes. Thus, phloreoxin (2), containing a biphenyl moiety catalyzed by A. bisporus polyphenol oxidase, have the potential to influence the anti-adipogenic capacity.

Phenylalanine Gold Nanoclusters as Sensing Platform for π-π Interfering Molecules: A Case Study of Lodide

The photo-physical properties of metal nano clusters are sensitive to their surrounding medium. Fluorescence enhancement, quenching, and changes in the emitted photon properties are usual events in the sensing applications using these nano materials. Combining this sensitivity with unique properties of self-assembled structures opens new opportunities for sensing applications. Here, we synthesized gold nanoclusters by utilizing phenylalanine amino acid as both capping and reducing molecule. Phenylalanine is able to self-assemble to rod-shaped nano structure in which the π-π interaction between the aromatic rings is a major stabilizing force. Any substance as iodide anion or molecule that is able to weaken this interaction influence the fluorescence of metal nano-clusters. Since the building blocks of the self-assembled structure are made through the reaction of gold ions and phenylalanine, the oxidized products and their effect of sensing features are explored.

Atmospheric organic vapors in two European pine forests measured by a Vocus PTR-TOF: insights into monoterpene and sesquiterpene oxidation processes

Atmospheric organic vapors play essential roles in the formation of secondary organic aerosol. Source identification of these vapors is thus fundamental to understanding their emission sources and chemical evolution in the atmosphere and their further impact on air quality and climate change. In this study, a Vocus proton-transfer-reaction time-of-flight mass spectrometer (PTR-TOF) was deployed in two forested environments, the Landes forest in southern France and the boreal forest in southern Finland, to measure atmospheric organic vapors, including both volatile organic compounds (VOCs) and their oxidation products. For the first time, we performed binned positive matrix factorization (binPMF) analysis on the complex mass spectra acquired with the Vocus PTR-TOF and identified various emission sources as well as oxidation processes in the atmosphere. Based on separate analysis of low- and high-mass ranges, 15 PMF factors in the Landes forest and nine PMF factors in the Finnish boreal forest were resolved, showing a high similarity between the two sites. Particularly, terpenes and various terpene reaction products were separated into individual PMF factors with varying oxidation degrees, such as lightly oxidized compounds from both monoterpene and sesquiterpene oxidation, monoterpene-derived organic nitrates, and monoterpene more oxidized compounds. Factors representing monoterpenes dominated the biogenic VOCs in both forests, with lower contributions from the isoprene factors and sesquiterpene factors. Factors of the lightly oxidized products, more oxidized products, and organic nitrates of monoterpenes/sesquiterpenes accounted for 8 %–12 % of the measured gas-phase organic vapors in the two forests. Based on the interpretation of the results relating to oxidation processes, further insights were gained regarding monoterpene and sesquiterpene reactions. For example, a strong relative humidity (RH) dependence was found for the behavior of sesquiterpene lightly oxidized compounds. High concentrations of these compounds only occur at high RH; yet similar behavior was not observed for monoterpene oxidation products.

Isoprostanes in Veterinary Medicine: Beyond a Biomarker

Oxidative stress has been associated with many pathologies, in both human and animal medicine. Damage to tissue components such as lipids is a defining feature of oxidative stress and can lead to the generation of many oxidized products, including isoprostanes (IsoP). First recognized in the early 1990s, IsoP are formed in numerous biological fluids and tissues, chemically stable, and easily measured by noninvasive means. Additionally, IsoP are highly specific indicators of lipid peroxidation and thereby are regarded as excellent biomarkers of oxidative stress. Although there have been many advancements in the detection and use of IsoP as a biomarker, there is still a paucity of knowledge regarding the biological activity of these molecules and their potential roles in pathology of oxidative stress. Furthermore, the use of IsoP has been limited in veterinary species thus far and represents an avenue of opportunity for clinical applications in veterinary practice. Examples of clinical applications of IsoP in veterinary medicine include use as a novel biomarker to guide treatment recommendations or as a target to mitigate inflammatory processes. This review will discuss the history, biosynthesis, measurement, use as a biomarker, and biological action of IsoP, particularly in the context of veterinary medicine.

Correction: Synthesis, crystal structure and antibacterial studies of dihydropyrimidines and their regioselectively oxidized products

Correction for ‘Synthesis, crystal structure and antibacterial studies of dihydropyrimidines and their regioselectively oxidized products’ by Alakbar E. Huseynzada et al., RSC Adv., 2021, 11, 6312–6329, DOI: 10.1039/D0RA10255E.

Synthesis, crystal structure and antibacterial studies of dihydropyrimidines and their regioselectively oxidized products

Known methods of synthesis of dihydropyrimidines and their oxidized products were modified, the impact of hydrogen bonds on stabilization of preferred tautomer and biological activities were studied.

A Comprehensive Review on Oxysterols and Related Diseases

: The present review aims to provide a complete and comprehensive summary of current literature relevant to oxysterols and related diseases. Oxidation of cholesterol leads to the formation of a large number of oxidized products, generally known as oxysterols. They are intermediates in the biosynthesis of bile acids, steroid hormones, and 1,25- dihydroxyvitamin D3. Although oxysterols are considered as metabolic intermediates, there is a growing body of evidence that many of them are bioactive, and their absence or excess may be part of the cause of a disease phenotype. These compounds derive from either enzymatic or non-enzymatic oxidation of cholesterol. This study provides comprehensive information about the structures, formation, and types of oxysterols even when involved in certain disease states, focusing on their effects on metabolism and linkages with these diseases. The role of specific oxysterols as mediators in various disorders, such as degenerative (age-related) and cancer-related disorders, has now become clearer. Oxysterol levels may be employed as suitable markers for the diagnosis of specific diseases or in predicting the incidence rate of diseases, such as diabetes mellitus, Alzheimer’s disease, multiple sclerosis, osteoporosis, lung cancer, breast cancer, and infertility. However, further investigations may be required to confirm these mentioned possibilities.