NAD(P)H-hydrate dehydratase- a metabolic repair enzyme and its role in Bacillus subtilis stress adaptation

Mechanisms of action of Fucus vesiculosus-derived fucoidan on improving dyslipidemia in New Zealand rabbits fed a high-fat diet

Dyslipidemia is a major contributor to various diseases, including atherosclerotic cardiovascular disease and obesity. Treatment strategies for dyslipidemia continue to evolve as our understanding of this metabolic disorder and potential therapeutic candidates advance. Notably, fucoidan demonstrates promising effects in ameliorating dyslipidemia in rodents, although their lipid metabolism differs significantly from humans. This study, investigates the lipid-regulatory effects of Fucus vesiculosus-derived fucoidan (FvF) and elucidates the underlying mechanisms of action using New Zealand rabbits fed a high-fat diet, whose lipid profiles closely resemble those of patients with dyslipidemia. The results demonstrate that FvF intervention ameliorates dyslipidemia and lipid deposition in a dose-dependent manner. Mechanistically, FvF intervention modulates the expression levels of multiple molecules involved in lipid transport, fatty acid synthesis and beta-oxidation, and redox balance, as revealed by quantitative reverse transcription polymerase chain reaction, western blotting, and proteomic analysis. This study is the first to report that FvF, consisting of alternating [→4)-α-L-Fucp(1 → 3)-α-L-Fucp(1→] glycosyls ameliorates dyslipidemia by directly modulating lipid metabolism and indirectly attenuating oxidative stress. These findings suggest that FvF holds significant potential as a candidate for the treatment of lipid disorder-related diseases.

Near-infrared laser-controlled nitric oxide-releasing gold nanostar/hollow polydopamine Janus nanoparticles for synergistic elimination of methicillin-resistant Staphylococcus aureus and wound healing

Recently, nitric oxide (NO) has received increasing interest in combat against bacteria-induced infections because of its ability to sensitize and enhance the antibacterial effectiveness of many therapeutic approaches such as antibiotics. However, high-efficient loading and controlled release of NO remain a big challenge. In the present work, a type of gold nanostar/hollow polydopamine Janus nanostructure (GNS/HPDA JNPs) with precise near infrared (NIR)-controlled NO release property was fabricated using a facile seed-mediated method. Upon NIR laser irradiation, the NO-releasing GNS/HPDA JNPs (GNS/HPDA-BNN6) exhibited a synergistic photothermal and NO antibacterial effect by significantly inhibiting the growth and biofilm formation of both Gram-negative and Gram-positive bacterial strains, including methicillin-resistant Staphylococcus aureus (MRSA). An in-depth mechanism study revealed that two pathways were mainly involved in the synergistic photothermal and NO antibacterial effect. In one pathway, the synergistic effect severely destroyed the bacterial membrane by causing leakage of intracellular components such as DNA. In another pathway, the synergistic effect largely disturbed bacterial metabolism by regulating relative metabolic genes, followed by enhancing ROS generation to cause intracellular GSH depletion and DNA damage. More importantly, the synergistic effect significantly diminished the drug resistance of MRSA by downregulating the expression of the drug-resistant gene mecA and some relative multidrug efflux pumps (e.g., SepA and Tet38). An in vivo evaluation using a rat model with MRSA-infected wounds indicated that the synergistic photothermal and NO effect of GNS/HPDA-BNN6 can effectively eliminate MRSA from wounds, thereby alleviating inflammation and promoting wound healing. STATEMENT OF SIGNIFICANCE: Multidrug-resistant (MDR) bacteria have become a big threat to mankind, and therefore, the development of innovative antibacterial agents with high antibacterial efficiency is urgently required. Nanomaterial-mediated nitric oxide (NO) therapy is a promising strategy to effectively combat MDR bacteria through a synergistic antibacterial effect. Here, a gold nanostar/hollow polydopamine Janus nanostructure with precise near infrared (NIR) light-controlled NO release property (GNS/HPDA-BNN6) was developed. Both in vitro and in vivo evaluations demonstrated that GNS/HPDA-BNN6 could effectively eliminate methicillin-resistant Staphylococcus aureus (MRSA) from infected wounds and promote wound healing through a synergistic photothermal and NO therapeutic effect. Remarkably, the synergistic effect significantly diminished the drug resistance of MRSA by downregulating the expression of some drug-resistant genes and multidrug efflux pumps.

Approaches for completing metabolic networks through metabolite damage and repair discovery

Metabolites are prone to damage, either via enzymatic side reactions, which collectively form the underground metabolism, or via spontaneous chemical reactions. The resulting non-canonical metabolites that can be toxic, are mended by dedicated "metabolite repair enzymes." Deficiencies in the latter can cause severe disease in humans, whereas inclusion of repair enzymes in metabolically engineered systems can improve the production yield of value-added chemicals. The metabolite damage and repair loops are typically not yet included in metabolic reconstructions and it is likely that many remain to be discovered. Here, we review strategies and associated challenges for unveiling non-canonical metabolites and metabolite repair enzymes, including systematic approaches based on high-resolution mass spectrometry, metabolome-wide side-activity prediction, as well as high-throughput substrate and phenotypic screens.

Acute pathophysiological myocardial changes following intra-cardiac electrical shocks using a proteomic approach in a sheep model

Implantable cardioverter-defibrillators (ICD) are meant to fight life-threatening ventricular arrhythmias and reduce overall mortality. Ironically, life-saving shocks themselves have been shown to be independently associated with an increased mortality. We sought to identify myocardial changes at the protein level immediately after ICD electrical shocks using a proteomic approach. ICD were surgically implanted in 10 individuals of a healthy male sheep model: a control group (N = 5) without any shock delivery and a shock group (N = 5) with the delivery of 5 consecutive shocks at 41 J. Myocardial tissue samples were collected at the right-ventricle apex near to the lead coil and at the right ventricle basal free wall region. Global quantitative proteomics experiments on myocardial tissue samples were performed using mass spectrometry techniques. Proteome was significantly modified after electrical shock and several mechanisms were associated: protein, DNA and membrane damages due to extreme physical conditions induced by ICD-shock but also due to regulated cell death; metabolic remodeling; oxidative stress; calcium dysregulation; inflammation and fibrosis. These proteome modifications were seen in myocardium both "near" and "far" from electrical shock region. N-term acetylated troponin C was an interesting tissular biomarker, significantly decreased after electrical shock in the "far" region (AUC: 0.93). Our data support an acute shock-induced myocardial tissue injury which might be involved in acute paradoxical deleterious effects such as heart failure and ventricular arrhythmias.

Interaction of zinc and IAA alleviate aluminum-induced damage on photosystems via promoting proton motive force and reducing proton gradient in alfalfa

BACKGROUND

In acidic soils, aluminum (Al) competing with Zn results in Zn deficiency in plants. Zn is essential for auxin biosynthesis. Zn-mediated alleviation of Al toxicity has been rarely studied, the mechanism of Zn alleviation on Al-induced photoinhibition in photosystems remains unclear. The objective of this study was to investigate the effects of Zn and IAA on photosystems of Al-stressed alfalfa. Alfalfa seedlings with or without apical buds were exposed to 0 or100 μM AlCl3 combined with 0 or 50 μM ZnCl2, and then foliar spray with water or 6 mg L- 1 IAA.

RESULTS

Our results showed that Al stress significantly decreased plant growth rate, net photosynthetic rate (Pn), quantum yields and electron transfer rates of PSI and PSII. Exogenous application of Zn and IAA significantly alleviated the Al-induced negative effects on photosynthetic machinery, and an interaction of Zn and IAA played an important role in the alleviative effects. After removing apical buds of Al-stressed alfalfa seedlings, the values of pmf, gH+ and Y(II) under exogenous spraying IAA were significantly higher, and ΔpHpmf was significantly lower in Zn addition than Al treatment alone, but the changes did not occur under none spraying IAA. The interaction of Zn and IAA directly increased Y(I), Y(II), ETRI and ETRII, and decreased O2- content of Al-stressed seedlings. In addition, the transcriptome analysis showed that fourteen functionally noted genes classified into functional category of energy production and conversion were differentially expressed in leaves of alfalfa seedlings with and without apical buds.

CONCLUSION

Our results suggest that the interaction of zinc and IAA alleviate aluminum-induced damage on photosystems via increasing pmf and decreasing ΔpHpmf between lumen and stroma.

Whole-cell based synthetic enzyme cascades-light and shadow of a promising technology

Mimicking Nature by biocatalytic cascade reactions in a whole-cell environment is a revolutionary development in multistep synthesis for the production of bulk and fine chemicals. In the past decade, several proof of concept success stories demonstrated the power of those synthetic cascades and paved the road for future industrial applications. Although enzymes and their promiscuity are best suited to construct such artificial pathways, the complexity and the lack of understanding of the cellular machinery slowed down this progress significantly. In this review, recent achievements in the field of whole-cell biocatalysis are described, challenges and hidden traps that have to be overcome are depicted, and strategies are illustrated how to increase overall cascade productivity.

NAD(P)HX repair deficiency causes central metabolic perturbations in yeast and human cells

NADHX and NADPHX are hydrated and redox inactive forms of the NADH and NADPH cofactors, known to inhibit several dehydrogenases in vitro. A metabolite repair system that is conserved in all domains of life and that comprises the two enzymes NAD(P)HX dehydratase and NAD(P)HX epimerase, allows reconversion of both the S- and R-epimers of NADHX and NADPHX to the normal cofactors. An inherited deficiency in this system has recently been shown to cause severe neurometabolic disease in children. Although evidence for the presence of NAD(P)HX has been obtained in plant and human cells, little is known about the mechanism of formation of these derivatives in vivo and their potential effects on cell metabolism. Here, we show that NAD(P)HX dehydratase deficiency in yeast leads to an important, temperature-dependent NADHX accumulation in quiescent cells with a concomitant depletion of intracellular NAD⁺ and serine pools. We demonstrate that NADHX potently inhibits the first step of the serine synthesis pathway in yeast. Human cells deficient in the NAD(P)HX dehydratase also accumulated NADHX and showed decreased viability. In addition, those cells consumed more glucose and produced more lactate, potentially indicating impaired mitochondrial function. Our results provide first insights into how NADHX accumulation affects cellular functions and pave the way for a better understanding of the mechanism(s) underlying the rapid and severe neurodegeneration leading to early death in NADHX repair-deficient children.

Label-free proteomic analysis to characterize ginger from China and Ghana

Ginger is a popular spice used in food and beverages. In this study, we sought to characterize and differentiate ginger samples of Ghana and China origin using label-free proteomic and untargeted metabolomic analyses. As result, a total of 180 proteins significantly changed between the ginger samples from both studied countries. Among them, 17 proteins were specifically identified in the Chinese ginger, while 23 proteins were only identified in the Ghanaian ginger. Function and bioinformatics analyses indicated that changes in carbon metabolism, secondary metabolites biosyntheses, citrate acid cycle, and amino acids biosyntheses-related pathways contributed to the differences. These results were confirmed through the identification of 14 significantly changed metabolites including diarylheptanoids and gingerols. Importantly, change tendencies of these metabolites corresponded to changes in abundance of the protein enzymes involved in their syntheses. These results suggest that changes in metabolism-related protein enzymes are responsible for the intraspecies difference of the ginger samples.

Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement

Genome annotation is, nowadays, performed via automatic pipelines that cannot discriminate between right and wrong annotations. Given their importance in increasing the accuracy of the genome annotations of other organisms, it is critical that the annotations of model organisms reflect the current annotation gold standard. The genome of Bacillus subtilis strain 168 was sequenced twenty years ago. Using a combination of inductive, deductive and abductive reasoning, we present a unique, manually curated annotation, essentially based on experimental data. This reveals how this bacterium lives in a plant niche, while carrying a paleome operating system common to Firmicutes and Tenericutes. Dozens of new genomic objects and an extensive literature survey have been included for the sequence available at the INSDC (AccNum AL009126.3). We also propose an extension to Demerec's nomenclature rules that will help investigators connect to this type of curated annotation via the use of common gene names.

Comparative Morphology, Transcription, and Proteomics Study Revealing the Key Molecular Mechanism of Camphor on the Potato Tuber Sprouting Effect

Sprouting regulation in potato tubers is important for improving commercial value and producing new plants. Camphor shows flexible inhibition of tuber sprouting and prolongs the storage period of potato, but its underlying mechanism remains unknown. The results of the present study suggest that camphor inhibition caused bud growth deformities and necrosis, but after moving to more ventilated conditions, new sprouts grew from the bud eye of the tuber. Subsequently, the sucrose and fructose contents as well as polyphenol oxidase (PPO) activity were assessed after camphor inhibition. Transcription and proteomics data from dormancy (D), sprouting (S), camphor inhibition (C), and recovery sprouting (R) samples showed changes in the expression levels of approximately 4000 transcripts, and 700 proteins showed different abundances. KEGG (Kyoto encyclopaedia of genes and genomes) pathway analysis of the transcription levels indicated that phytohormone synthesis and signal transduction play important roles in tuber sprouting. Camphor inhibited these processes, particularly for gibberellic acid, brassinosteroids, and ethylene, leading to dysregulation of physiological processes such as cutin, suberine and wax biosynthesis, fatty acid elongation, phenylpropanoid biosynthesis, and starch and sucrose metabolism, resulting in bud necrosis and prolonged storage periods. The KEGG pathway correlation between transcripts and proteins revealed that terpenoid backbone biosynthesis and plant-pathogen interaction pathways showed significant differences in D vs. S samples, but 13 pathways were remarkably different in the D vs. C groups, as camphor inhibition significantly increased both the transcription levels and protein abundance of pathogenesis-related protein PR-10a (or STH-2), the pathogenesis-related P2-like precursor protein, and the kirola-like protein as compared to sprouting. In recovery sprouting, these genes and proteins were decreased at both the transcriptional level and in protein abundance. It was important to find that the inhibitory effect of camphor on potato tuber sprout was reversible, revealing the action mechanism was similar to resistance to pathogen infection. The present study provides a theoretical basis for the application of camphor in prolonging seed potato storage.