Ecotoxicological impact of butisanstar and clopyralid herbicides on soil microbial respiration and the enzymatic activities

The application of herbicides in soil has been noted for its detrimental effect on the soil microbial community, crucial for various biochemical processes. This study provides a comprehensive assessment of the impact of butisanstar and clopyralid herbicides, both individually and in combination at different dosage (recommended field dose (RFD), ½, 2 and 5-times RFD). The assessment focuses on soil basal respiration (SBR), cumulative microbial respiration (CMR), and the activities dehydrogenase (DH), catalase (CAT), urease, acid and alkaline phosphatases (Ac-P and Alk-P) enzymes, along with their variations on days 10, 30, 60, and 90 post-herbicide application. Results indicate that, although herbicides, even at lower doses of RFD, demonstrate inhibitory effects on DH, CAT, and microbial respiration, they paradoxically lead to a significant enhancement in urease and phosphatase activities, even at higher doses. The inhibitory/enhancing intensity varies based on herbicide type, incubation period, and dosage. Co-application of herbicides manifests synergistic effects compared to individual applications. The most notable inhibitory effects on DH, CAT, and SBR are observed on the 30th day, coinciding with the highest activities of urease and phosphatases on the same day. The persistent inability to restore respiration and enzyme activities to initial soil (control) levels emphasizes the lasting adverse and inhibitory effects of herbicides, especially clopyralid, over the long term. It becomes apparent that soil microorganisms require an extended duration to decompose and acclimate to the presence of herbicides. Consequently, these agrochemical compounds pose a potential risk to crucial biochemical processes, such as nutrient cycling, ultimately impacting crop production.

Evaluation of the first 5 years of a glutaric aciduria type I neonatal screening programme in Asturias

INTRODUCTION

. Neonatal screening of glutaric aciduria type 1 (GA-1) has brought radical changes in the course and outcomes of this disease. This study analyses the outcomes of the first 5 years (2015-2019) of the AGA1 neonatal screening programme in our autonomous community.

MATERIAL

. We conducted an observational, descriptive and retrospective study. All neonates born between January 1, 2015 and December 31, 2019 that participated in the neonatal screening programme were included in the study. The glutarylcarnitine (C5DC) concentration in dry blood spot samples was measured by means of tandem mass spectrometry applying a cut-off point of 0.25 µmol/L.

RESULTS

. A total of 30 120 newborns underwent screening. We found differences in the C5DC concentration based on gestational age, type of feeding and hours of life at sample collection. These differences were not relevant for screening purposes. There were no differences between neonates with weights smaller and greater than 1500 g. Screening identified 2 affected patients and there were 3 false positives. There were no false negatives. The diagnosis was confirmed by genetic testing. Patients have been in treatment since diagnosis and have not developed encephalopathic crises in the first 4 years of life.

CONCLUSIONS

. Screening allowed early diagnosis of two cases of GA-1 in the first 5 years since its introduction in our autonomous community. Although there were differences in C5DC levels based on gestational age, type of feeding and hours of life at blood extraction, they were not relevant for screening.

Physio-biochemical responses and crop performance analysis in chickpea upon botanical priming

Chickpea is a highly nutritious protein-rich source and one of the major crops to alleviate global malnutrition, but poor seed quality affects its productivity. Seed quality is essential for better crop establishment and higher yields, particularly in the uncertain climate change. The present study investigated the impact of botanical priming versus hydropriming and bavistin seed treatment on chickpea seeds. A detailed physiological (germination percentage, root and shoot length, vigour index) and biochemical (amylase, protease, dehydrogenase, phytase, and lipid peroxidation) analysis was carried out in order to assess the effect of priming treatments. Turmeric-primed seeds showed better germination rate (94.5%), seedling length, enzyme activity, and lower malondialdehyde (MDA) content. Sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis revealed the expression of minor polypeptides of albumin and globulin in the primed seeds. Moreover, field experiments indicated increased crop growth, vigour, days to 50% flowering, yield and its attributing traits in turmeric-primed seeds. Botanical priming can increase chickpea yield by up to 16% over the control group. This low-cost and eco-friendly technique enhances seed and crop performance, making it a powerful tool for augmenting chickpea growth. Therefore, chickpea growers must adopt botanical priming techniques to enhance the quality of seed and crop performance. Moreover, this approach is environmentally sustainable and can help conserve natural resources in the long term. Therefore, this new approach must be widely adopted across the agricultural industry to ensure sustainable and profitable farming practices.

AraC transcriptional regulator, aspartate semialdehyde dehydrogenase and acyltransferase: Three putative genes in phenol catabolic pathway of Acinetobacter sp. Strain DF4

The objective of this study was to identify genes associated with the biodegradation of phenol by Acinetobacter sp. strain DF4 through the use of differential display (DD) methodology. The bacteria were grown in YEPG medium, and total RNA was extracted and analyzed using labeled primers to detect gene expression differences. Three distinctively expressed cDNA bands (ph1, ph2, and ph3) were identified, cloned, and sequenced. DNA analysis involved searching for open reading frames (ORFs), verifying results with the NCBI database, predicting promoter regions, and constructing phylogenetic trees using bioinformatics tools. The ph1 gene displayed a 97% identity with the AraC transcriptional regulator, suggesting its potential role in regulating the ortho-catabolic pathway of phenol. The ph2 gene showed a 98% identity with aspartate semialdehyde dehydrogenase, which is involved in phenol degradation. The ph3 gene had a 93% identity with acetyltransferase. Essential transcription factors, such as TATA, GTGTGT, CACA, and CTTTT, were detected, and the three genes promoter regions were predicted. This study successfully identified functional genes involved in the metabolism of cyclic chemicals, particularly phenol, using the DD technique. These findings provide insights into the biodegradation pathways of phenol by Acinetobacter sp. Strain DF4 and may contribute to the development of more efficient bioremediation strategies for phenol-contaminated environments.

A gene therapy targeting medium-chain acyl-CoA dehydrogenase (MCAD) did not protect against diabetes-induced cardiac pathology

Diabetic cardiomyopathy describes heart disease in patients with diabetes who have no other cardiac conditions but have a higher risk of developing heart failure. Specific therapies to treat the diabetic heart are limited. A key mechanism involved in the progression of diabetic cardiomyopathy is dysregulation of cardiac energy metabolism. The aim of this study was to determine if increasing the expression of medium-chain acyl-coenzyme A dehydrogenase (MCAD; encoded by Acadm), a key regulator of fatty acid oxidation, could improve the function of the diabetic heart. Male mice were administered streptozotocin to induce diabetes, which led to diastolic dysfunction 8 weeks post-injection. Mice then received cardiac-selective adeno-associated viral vectors encoding MCAD (rAAV6:MCAD) or control AAV and were followed for 8 weeks. In the non-diabetic heart, rAAV6:MCAD increased MCAD expression (mRNA and protein) and increased Acadl and Acadvl, but an increase in MCAD enzyme activity was not detectable. rAAV6:MCAD delivery in the diabetic heart increased MCAD mRNA expression but did not significantly increase protein, activity, or improve diabetes-induced cardiac pathology or molecular metabolic and lipid markers. The uptake of AAV viral vectors was reduced in the diabetic versus non-diabetic heart, which may have implications for the translation of AAV therapies into the clinic. KEY MESSAGES: The effects of increasing MCAD in the diabetic heart are unknown. Delivery of rAAV6:MCAD increased MCAD mRNA and protein, but not enzyme activity, in the non-diabetic heart. Independent of MCAD enzyme activity, rAAV6:MCAD increased Acadl and Acadvl in the non-diabetic heart. Increasing MCAD cardiac gene expression alone was not sufficient to protect against diabetes-induced cardiac pathology. AAV transduction efficiency was reduced in the diabetic heart, which has clinical implications.

Human peroxisomal NAD+/NADH homeostasis is regulated by two independent NAD(H) shuttle systems

Reduced (NADH) and oxidized (NAD+) nicotinamide adenine dinucleotides are ubiquitous hydride-donating/accepting cofactors that are essential for cellular bioenergetics. Peroxisomes are single-membrane-bounded organelles that are involved in multiple lipid metabolism pathways, including beta-oxidation of fatty acids, and which contain several NAD(H)-dependent enzymes. Although maintenance of NAD(H) homeostasis in peroxisomes is considered essential for peroxisomal beta-oxidation, little is known about the regulation thereof. To resolve this issue, we have developed methods to specifically measure intraperoxisomal NADH levels in human cells using peroxisome-targeted NADH biosensors. By targeted CRISPR-Cas9-mediated genome editing of human cells, we showed with these sensors that the NAD+/NADH ratio in cytosol and peroxisomes are closely connected and that this crosstalk is mediated by intraperoxisomal lactate and malate dehydrogenases, generated via translational stop codon readthrough of the LDHB and MDH1 mRNAs. Our study provides evidence for the existence of two independent redox shuttle systems in human peroxisomes that regulate peroxisomal NAD+/NADH homeostasis. This is the first study that shows a specific metabolic function of protein isoforms generated by translational stop codon readthrough in humans.

Biochar alleviated the toxic effects of PVC microplastic in a soil-plant system by upregulating soil enzyme activities and microbial abundance

Plastics have become an emerging pollutant threatening the sustainability of agroecosystems and global food security. Biochar, a pro-ecosystem/negative carbon emission technology can be exploited as a circular approach for the conservation of plastics contaminated agricultural soils. However, relatively few studies have focused on the effects of biochar on plant growth and soil biochemical properties in a microplastic contaminated soil. This study investigated the effects of a cotton stalk (Gossypium hirsutum L.) biochar on plant growth, soil microbes, and enzyme activity in PVC microplastic (PVC-MPs) contaminated soil. Biochar amendment increased shoot dry matter production in PVC-MPs contaminated soil. However, PVC-MPs alone significantly reduced the soil urease and dehydrogenase activity, soil organic and microbial biomass carbon, bacterial/fungal community percentage, and their abundance (16S rRNA and 18S rRNA genes, respectively). Interestingly, biochar amendment with PVC-MPs significantly alleviated the hazardous effects. Principal component and redundancy analysis of the soil properties, bacterial 16S rRNA genes, and fungal ITS in the biochar-amended PVC-MPs treatments revealed that the observed traits formed an obvious cluster compared to non-biochar treatments. To sum up, this study indicated that PVC-MPs contamination was not benign, while biochar shielded the hazardous effects and sustained soil microbial functionality.

Combinatorial gene inactivation of aldehyde dehydrogenases mitigates aldehyde oxidation catalyzed by E. coli resting cells

Aldehydes are attractive chemical targets both as end products in the flavors and fragrances industry and as intermediates due to their propensity for C-C bond formation. Here, we identify and address unexpected oxidation of a model collection of aromatic aldehydes, including many that originate from biomass degradation. When diverse aldehydes are supplemented to E. coli cells grown under aerobic conditions, as expected they are either reduced by the wild-type MG1655 strain or stabilized by a strain engineered for reduced aromatic aldehyde reduction (the E. coli RARE strain). Surprisingly, when these same aldehydes are supplemented to resting cell preparations of either E. coli strain, under many conditions we observe substantial oxidation. By performing combinatorial inactivation of six candidate aldehyde dehydrogenase genes in the E. coli genome using multiplexed automatable genome engineering (MAGE), we demonstrate that this oxidation can be substantially slowed, with greater than 50% retention of 6 out of 8 aldehydes when assayed 4 h after their addition. Given that our newly engineered strain exhibits reduced oxidation and reduction of aromatic aldehydes, we dubbed it the E. coli ROAR strain. We applied the new strain to resting cell biocatalysis for two kinds of reactions - the reduction of 2-furoic acid to furfural and the condensation of 3-hydroxy-benzaldehyde and glycine to form a beta hydroxylated non-standard amino acid. In each case, we observed substantial improvements in product titer 20 h after reaction initiation (9-fold and 10-fold, respectively). Moving forward, the use of this strain to generate resting cells should allow aldehyde product isolation, further enzymatic conversion, or chemical reactivity under cellular contexts that better accommodate aldehyde toxicity.

Climate and edaphic factors drive soil enzyme activity dynamics and tolerance to Cd toxicity after rewetting of dry soil

The intense drying-rewetting cycle due to climate change can affect soil microbial community composition and function, resulting in long-term consequences for belowground carbon and nutrient dynamics. However, how climatic and edaphic factors influence the responses of enzymes to rewetting and their responses to additional perturbation (e.g., heavy metal pollution) after the drying-rewetting history are not well understood. In this study, we collected 18 surface soils from farmlands across various climate zones in China. We chose dehydrogenase (DHA) and alkaline phosphomonoesterase (ALP) as representative intracellular and extracellular enzymes, respectively, and investigated their tolerance to additional perturbation by adding metal ions (i.e., Cd²⁺) upon rewetting. In all soils, rewetting increased DHA activities but did not affect ALP activities compared to air-dried soils. Rewetting increased the tolerances of DHA and ALP to Cd stress, suggesting that the drying-rewetting history may reduce the susceptibility of soil enzymes to additional disturbance. The results demonstrate that differentiating enzymes based on their location in the soil will improve our ability to assess the stress response of microbial communities to drastic fluctuations in soil moisture, thereby better predicting the legacy of climate change on microbial function in soils contaminated with heavy metals.

Isocitrate Dehydrogenase Mutations Are Associated with Different Expression and DNA Methylation Patterns of OLIG2 in Adult Gliomas

Isocitrate dehydrogenase (IDH) mutant gliomas are associated with a better prognosis in comparison to adult IDH wild-type glioma and glioma-CpG island methylator phenotypes. Although OLIG2 is mainly expressed in oligodendrocytes in normal adult brain, it is expressed in both astrocytomas and oligodendrogliomas. Utilizing the clinical, DNA methylation, and RNA-sequencing data from the Cancer Genome Atlas (TCGA) for lower-grade glioma and glioblastoma cohorts, we explored the association between IDH mutation status and OLIG2 expression on transcription, DNA methylation, and gene target levels. Compared to IDH wild-type gliomas, IDH mutant gliomas showed consistently higher expression of OLIG2 transcripts. OLIG2 overexpression is a good surrogate marker for IDH mutation with an AUC of 0.90. At the DNA methylation level, IDH-mutant gliomas showed hyper- and hypomethylation foci upstream of the OLIG2 transcription start site. Underexpressed OLIG2 target genes in IDH mutant glioma were enriched in cell cycle-related pathways. Thus, the differential expression of OLIG2 between IDH mutant and wild-type gliomas reflects involvement in multiple pathways in tumorigenesis.

Integrative analyses of geochemical parameters-microbe interactions reveal the variation of bacterial community assembly in multiple metal(loid)s contaminated arable regions

Soil microbes play crucial roles in biochemical and geochemical processes in contaminated arable ecosystems. However, what factors determine the assembling process of soil bacterial community under multiple heavy metal (loid)s (HMs) stress and how communities respond to geochemical changes have rarely been understood. Therefore, a number of contaminated soils were sampled to explore the interactions among geochemical parameters, HMs and innate bacterial community. The results showed that soil biochemical activities were inhibited obviously with the increase of HMs. Significant differences were observed in bacterial composition and abundance in studied areas, with Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria and Firmicutes governing the bacterial community structure. Redundancy analysis and variation partition analysis revealed that about 67.33% of the variation in bacterial assemblages could be explained by physiochemical parameters (21.59%), biochemical parameters (11.64%), toxic metal (loid)s (9.11%) and the interaction effect of these variables (24.99%), among which total-arsenic and moisture were the main factors. Spearman correlation analysis also demonstrated that dehydrogenase, moisture and TOC have a positive correlation with bacterial community structure with As-Cd-Pb gradient. Altogether, this study would provide a comprehensive relationship between major environmental factors and bacterial assemblages, which could offer some baseline data to investigate the mechanisms of how communities respond to physiochemical changes.

Controllably crosslinked dual enzymes enabled by genetic-encoded non-standard amino acid for efficiently enantioselective hydrogenation

In traditional method for preparing crosslinked enzymes aggregates using glutaraldehyde, random linkage is inevitable, which often destroys the enzyme active sites and severely decreases the activity. To address this issue, using genetic encode expanding, nonstandard amino acids (NSAAs) were inserted into enzyme proteins at the preselected sites for crosslinking. When aldehyde ketone reductase (AKR), alcohol dehydrogenase (ADH) and glucose dehydrogenase (GDH) were utilized as model enzymes, their mutants containing p-azido-L-phenylalanine were bio-orthogonally crosslinked with diyne to form crosslinked dual enzymes (CLDEs) acting as a cascade biological oxidation and reduction system. Then, the resultant self-purified CLDEs were characterized using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM), etc. In the asymmetric synthesis of (S)-1-(2,6-dichloro-3-fluorophenyl) ethanol using CLDEs, high product yield (76.08%), ee value (99.99%) and reuse stability were achieved. The yield and ee value were 12.05 times and 1.39 times higher than those using traditional crosslinked enzyme aggregates, respectively. Thus, controllable insertion NSAAs in number and location can engender reasonable linkage and metal-free self-purification for target enzyme proteins. This facile and sustainable method could be further expanded to other dual and multienzyme systems for cascade biocatalysis.

Soil organic matter and biological activity under long-term contamination with copper

Organic matter (OM) and enzymes activity can act as indicators of the time and level of soil contamination with heavy metal. The goal of this study is evaluation of the effect of chronic long-term soil contamination with Cu on OM and biological activity in Spolic Technosols. The monitoring plot is located in the zone of industrial wastewater storage and sludge reservoirs in the Seversky Donets River flood plain. The total amount of Cu in the investigated soils varied greatly from 52 to 437 mg/kg. The results of Cu sequential fractionation the contaminated soil have shown that the chemical fraction composition of metal changed when the soil contamination level increased. The amount of Cu compounds associated with OM and Fe and Mn oxides was also higher. Fractions of OM from the humic and fulvic acids groups were studied. Soil was subjected to extraction with cold and hot water, and the content of water-soluble OM (WSOM) was determined. An increased solubility of humic and fulvic acids as well as elevated content of cold and hot extraction WSOM was established. The cold-extracted amount of WSOM increased with an enhance in the Cu content. The long-term contamination of soil with Cu leads to an adaptation of microorganisms to this adverse environmental factor, and this adaptation is manifested in the WSOM content increase. The effect of Cu contamination on microbiological activity was assessed by plate-counting culturable microorganisms and determining urease and dehydrogenase enzymatic activity. A high level of soil contamination with Cu showed a noticeable negative effect on the number of soil bacteria; however, active and potentially active bacteria were observed even in the highly contaminated soils. The changes in soil OM and microbial communities caused by Cu pollution can lead to disruption of ecosystem functioning.

Fungal pretreatment facilitates the rapid and valuable composting of waste cardboard

This study investigates the waste cardboard (WCB) fungal pretreatment (Oligoporus placenta and Tremetes hirsuta) under monoculture and mixed culture and then composting for 35 d after mixing with cow dung in different ratios. Fungal pretreatment caused significant reduction in cellulose (28.3-35.8%), hemicellulose (61.4-68.4%), lignin (67.5-69.3%) content in WCB. Pretreated WCB showed better rates of decrement in total organic carbon (26.02-47.92%), carbon-to-nitrogen ratio (19.4-23.5), and lignocellulose contents, as well as incensement in total nitrogen (40.48-63.31%), total potassium (51.92-73.91%), germination index (88.5-102.0%), and elemental (Cu, Fe, Zn, Cr, and Mn) levels. Dehydrogenases (142-210 µg g^-1h^-1), and β-galactosidase (210-256 µg g^-1h^-1) activities indicates high microbial-mediated mineralization in setups. Results suggested that WCB could be used as a valuable substrate for valuable-added compost preparation after pretreating with a consortium of white-rot fungi.

Selectivity of enzymes involved in the formation of opposite enantiomeric series of p-menthane monoterpenoids in peppermint and Japanese catnip

Peppermint (Mentha x piperita L.) and Japanese catnip (Schizonepeta tenuifolia (Benth.) Briq.) accumulate p-menthane monoterpenoids with identical functionalization patterns but opposite stereochemistry. In the present study, we investigate the enantioselectivity of multiple enzymes involved in monoterpenoid biosynthesis in these species. Based on kinetic assays, mint limonene synthase, limonene 3-hydroxylase, isopiperitenol dehydrogenase, isopiperitenone reductase, and menthone reductase exhibited significant enantioselectivity toward intermediates of the pathway that proceeds through (-)-4S-limonene. Limonene synthase, isopiperitenol dehydrogenase and isopiperitenone reductase of Japanese catnip preferred intermediates of the pathway that involves (+)-4R-limonene, whereas limonene 3-hydroxylase was not enantioselective, and the activities of pulegone reductase and menthone reductase were too low to acquire meaningful kinetic data. Molecular modeling studies with docked ligands generally supported the experimental data obtained with peppermint enzymes, indicating that the preferred enantiomer was aligned well with the requisite cofactor and amino acid residues implicated in catalysis. A striking example for enantioselectivity was peppermint (-)-menthone reductase, which binds (-)-menthone with exquisite affinity but was predicted to bind (+)-menthone in a non-productive orientation that positions its carbonyl functional group at considerable distance to the NADPH cofactor. The work presented here lays the groundwork for structure-function studies aimed at unraveling how enantioselectivity evolved in closely related species of the Lamiaceae and beyond.

Mammalian dihydropyrimidine dehydrogenase

Dihydropyrimidine dehydrogenase (DPD) catalyzes the two-electron reduction of pyrimidine bases uracil and thymine as the first step in pyrimidine catabolism. The enzyme achieves this simple chemistry using a complex cofactor set including two flavins and four Fe₄S₄ centers. The flavins, FAD and FMN, interact with respective NADPH and pyrimidine substrates and the iron-sulfur centers form an electron transfer wire that links the two active sites that are separated by 56 Å. DPD accepts the common antineoplastic agent 5-fluorouracil as a substrate and so undermines the establishment of efficacious toxicity. Though studied for multiple decades, a precise description of the behavior of the enzyme had remained elusive. It was recently shown that the active form of DPD has the cofactor set of FAD-4(Fe₄S₄)-FMNH₂. This two-electron reduced state is consistent with fewer mechanistic possibilities and data suggests that the instigating and rate determining step in the catalytic cycle is reduction of the pyrimidine substrate that is followed by relatively rapid oxidation of NADPH at the FAD that, via the electron conduit of the 4(Fe₄S₄) centers, reinstates the FMNH₂ cofactor for subsequent catalytic turnover.

Primary saturation of α, β-unsaturated carbonyl containing fatty acids does not abolish electrophilicity

Metabolism of polyunsaturated fatty acids results in the formation of hydroxylated fatty acids that can be further oxidized by dehydrogenases, often resulting in the formation of electrophilic, α,β-unsaturated ketone containing fatty acids. As electrophiles are associated with redox signaling, we sought to investigate the metabolism of the oxo-fatty acid products in relation to their double bond architecture. Using an untargeted liquid chromatography mass spectrometry approach, we identified mono- and di-saturated products of the arachidonic acid-derived 11-oxoeicosatetraenoic acid (11-oxoETE) and mono-saturated metabolites of 15-oxoETE and docosahexaenoic acid-derived 17-oxodocosahexaenoinc acid (17-oxoDHA) in both human A549 lung carcinoma and umbilical vein endothelial cells. Notably, mono-saturated oxo-fatty acids maintained their electrophilicity as determined by nucleophilic conjugation to glutathione while a second saturation of 11-oxoETE resulted in a loss of electrophilicity. These results would suggest that prostaglandin reductase 1 (PTGR1), known only for its reduction of the α,β-unsaturated double bond, was not responsible for the saturation of oxo-fatty acids at alternative double bonds. Surprisingly, knockdown of PTGR1 expression by shRNA confirmed its participation in the formation of 15-oxoETE and 17-oxoDHA mono-saturated metabolites. Furthermore, overexpression of PTGR1 in A549 cells increased the rate and total amount of oxo-fatty acid saturation. These findings will further facilitate the study of electrophilic fatty acid metabolism and signaling in the context of inflammatory diseases and cancer where they have been shown to have anti-inflammatory and anti-proliferative signaling properties.

Kinetic characterization and thermostability of C. elegans cytoplasmic and mitochondrial malate dehydrogenases

Malate dehydrogenase (MDH) catalyzes the conversion of NAD⁺ and malate to NADH and oxaloacetate in the citric acid cycle. Eukaryotes have one MDH isozyme that is imported into the mitochondria and one in the cytoplasm. We overexpressed and purified Caenorhabditis elegans cytoplasmic MDH-1 and mitochondrial MDH-2 in E. coli. Our goal was to compare the kinetic and structural properties of these enzymes because C. elegans can survive adverse environmental conditions, such as lack of food and elevated temperatures. In steady-state enzyme kinetics assays, we measured K_M values for oxaloacetate of 54 and 52 μM and K_M values for NADH of 61 and 107 μM for MDH-1 and MDH-2, respectively. We partially purified endogenous MDH-1 and MDH-2 from a mixed population of worms and separated them using anion exchange chromatography. Both endogenous enzymes had a K_M for oxaloacetate similar to that of the corresponding recombinant enzyme. Recombinant MDH-1 and MDH-2 had maximum activity at 40 °C and 35 °C, respectively. In a thermotolerance assay, MDH-1 was much more thermostable than MDH-2. Protein homology modeling predicted that MDH-1 had more intersubunit salt-bridges than mammalian MDH1 enzymes, and these ionic interactions may contribute to its thermostability. In contrast, the MDH-2 homology model predicted fewer intersubunit ionic interactions compared to mammalian MDH2 enzymes. These results suggest that the increased stability of MDH-1 may facilitate its ability to remain active in adverse environmental conditions. In contrast, MDH-2 may use other strategies, such as protein binding partners, to function under similar conditions.

Biotransformation of linoleic acid into different metabolites by food derived Lactobacillus plantarum 12-3 and in silico characterization of relevant reactions

Lactic acid bacteria have been reported to be capable of converting polyunsaturated fatty acids, e.g. linoleic acid (LA) into bioactive and other fatty acid metabolites that are not toxic to the bacteria themselves, but the mechanism of this conversion is not clear. Here we reported for the first time that probiotic L. plantarum 12-3 derived from Tibet kefir when supplemented with LA from 1% to 10% in the MRS medium transformed LA to various fatty acid derivatives. These derivatives formed in the medium were identified with gas chromatography and mass spectrometry. In silico studies were done to confirm the enzymatic reactions responsible for this conversion. We found that L. plantarum 12-3 could convert LA at different concentrations to 8 different fatty acid derivatives. Putative candidate enzymes involved in biotransformation of LA into fatty acid derivatives were identified via whole genome of L. plantarum 12-3, including linoleate isomerase, acetoacetate decarboxylase and dehydrogenase. Therefore, the present study provides further understanding of the mechanism of conversion of LA to health-beneficial fatty acid metabolites in probiotic L. plantarum, which can be explored for potential application in functional foods.

Applying enzymatic biomarkers of the in situ microbial community to assess the sediment risk from Sepetiba Bay (Brazil)

The Quality Ratio (QR) index was applied in Sepetiba Bay to integrate geochemical and microbiological parameters of the in situ microbial community in order to classify the ecological risk of sediments. Total concentrations (C) of Hg, Cd, As, Pb, Cr, Cu and Zn (indicators of the mixture of contaminants) were determined at 26 stations and at a background area (C₀) to calculate the contamination factor (CF = C/C₀) and the degree of contamination (ΣCF). Enzymatic biomarkers of energy production into cell (dehydrogenase - DHA) and hydrolase of organic matter outside the cell (esterases - EST) were determined. The QR, a function of the microbial term (DHA/EST) and the geochemical term (TOC × ΣCF/fine-grained content), was able to segregate stations into the internal sector (east of the bay with the largest continental contributions) and the external sector (west of the bay), proving its accessibility (low-cost and fast) and efficiency for assessing ecological risk.

Tryptophanase gene deficiency improves the application of dioxygenase to 3-(2-hydroxyethyl)catechol production

3-(2-Hydroxyethyl)catechol (HEC) is a polyphenol reported to exhibit skin-lightning and antioxidative effects, and hence is expected to be used as cosmetic and food additives and chemical products such as electronic materials. In this study, we established biocatalytic HEC production from 2-phenylethanol using the dioxygenase whose expression was induced by toluene, CumA, and its flanking dehydrogenase, CumB, from an isolated strain, Pseudomonas sp. K17. Escherichia coli cells coexpressing CumA and CumB were stained blue during cultivation in Luria-Bertani medium, and HEC was not produced upon using the cell-free extracts as biocatalysts, likely resulting from the inhibitory effects of the blue dyes. The disruption of the tryptophanase gene of E. coli was found to repress the generation of the blue dyes, and enhanced HEC production. The blue dyes were extracted from the cell-free extracts, and their molecular formula was C₁₆H₁₀N₂O₃, suggesting they were monooxygenated indigo or its isomers. Although repression of blue dye formation and enhancement of HEC production were observed when cells were cultivated with glucose, the percent yield of HEC was 84% at 20 h, whereas that with tryptophanase disruption strain was 84% at 4 h. It was suggested that tryptophanase gene disruption could contribute to more efficient HEC production.

Identification and characterization of Nornicotine degrading strain Arthrobacter sp. NOR5

Nornicotine, the primary nicotine metabolite that is formed through demethylation of nicotine in the genus Nicotiana tabacum L. Nornicotine is not only a precursor of tobacco-specific nitrosamine N-nitrosonornicotine but also have detrimental effects to human health. Till now, information on the biotransformation of nornicotine is limited. Herein, we identified and characterized a bacterium Arthrobacter sp. strain NOR5, utilized nornicotine as the sole of carbon and energy source, and degraded 500 mg/L nornicotine completely within 60 h under the optimum conditions of pH 7.0 and 30 °C. In this study, we not only identified previously reported intermediate metabolites such as 6-OH-nornicotine, 6-OH-mysomine, 6-OH-pseudooxy-nornicotine (6HPONor) but also identified a new intermediate metabolite 2,6-di-OH-pseudooxy-nornicotine (2,6DHPONor) by UV spectroscopy and liquid chromatography coupled with time of flight mass spectrometry. About half of 6HPONor could be transformed into 2,6DHPONor that was identified as a novel catabolic intermediate of nornicotine. By the addition of an electron acceptor 2,6-dichlorophenolindophenol (DCIP), the cell-free extract exhibited inducible 6HPONor dehydrogenase activity at 179 ± 60 mU/mg that could convert 6HPONor to 2,6DHPONor. Our study demonstrated that Arthrobacter sp. strain NOR5 has a high potential to degrade the nornicotine completely.

Metabolism of Carotenoids in Mammals

Pathways for xanthophyll metabolism have been proposed on the basis of several oxidation products of dietary xanthophylls detected in the tissues of fish, birds, and human subjects. No enzyme reaction had been characterized as responsible for the pathways until a mouse liver homogenate was found to oxidize the 3-hydroxy β-end of xanthophylls to a 3-oxo ε-end in the presence of a cofactor, NAD⁺. This oxidation consists of dehydrogenation to an unstable intermediate having a 3-oxo β-end group and the subsequent migration of a double bond. β,ε-Caroten-3'-one, a metabolite of β-cryptoxanthin, was found in human plasma, indicating that the same oxidative activity as that found in the mouse liver works in human tissues.The oxidative cleavage of carotenoids is mediated by two dioxygenases: a central cleavage enzyme and an asymmetric cleavage enzyme. In mice, the latter enzyme was suggested to eliminate carotenoids in tissues, while in humans, this enzyme is inactivated, resulting in carotenoid accumulation. In this chapter, carotenoid metabolism in mammals is described in terms of the oxidation of functional groups and cleavage of the carbon skeleton.

Catabolic enzyme activities during biodegradation of three-ring PAHs by novel DTU-1Y and DTU-7P strains isolated from petroleum-contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants having health hazards. PAH-utilizing bacterial strains were isolated from petroleum-contaminated soil from siding area, Bijwasan supply location of BPCL, Delhi, India. Bacterial strains with different morphology were isolated and acclimatized to a mixture of low molecular weight PAH compounds in the concentration range of 50-10,000 mg/L. Two bacterial strains surviving at 10,000 mg/L PAH concentration were identified as Kocuria flava and Rhodococcus pyridinivorans, based on 16S rRNA gene sequencing and phylogenetic analysis over MEGA X, are reported for the first time for PAH degradation. The strain K. flava could degrade phenanthrene, anthracene, and fluorene with efficiency of 55.13%, 59.01%, and 63.46%, whereas R. pyridinivorans exhibited 62.03%, 64.99%, and 66.79% degradation for respective PAHs at initial PAH concentration of 10 mg/L. Slightly lower degradation of phenanthrene could be attributed to its more stable chemical structure. The consortium of both the strains degraded 61.32%, 64.72%, and 66.64%, of 10 mg/L of phenanthrene, anthracene, and fluorene, respectively, in 15 days of incubation period indicating no synergistic or antagonistic effect towards degradation. Catechol 2,3-dioxygenase (C23O), dehydrogenase and peroxidase enzyme activities during PAH degradation coincided with degradation of PAHs, thus highlighting the role of these enzymes in catabolising three-ring PAHs. This is the first investigation confirming the participation of C23O, dehydrogenase and peroxidases enzyme profiles throughout the period of degradation. The study concludes that these strains can play significant role in microbial remediation of PAH-contaminated environment.

The influence of long-term Zn and Cu contamination in Spolic Technosols on water-soluble organic matter and soil biological activity

Potentially toxic elements (PTE) pollution has a pronounced negative effect on the soil and its components. The characteristics of soil organic matter and the activity of soil enzymes can serve as sensitive indicators of the degree of changes occurring in the soil. This study aims to assess the effect of long-term severe soil contamination with Zn and Cu on water-soluble organic matter (WSOM) and the associated changes in the biochemical activity of microorganisms. The total content of Zn and Cu in the studied soils varies greatly: Zn from 118 to 65,311 mg/kg, Cu from 52 to 437 mg/kg. The content of WSOM was determined using cold and hot extraction. It was revealed that the WSOM, extracted with cold water is a sensitive indicator reflecting the nature of the interaction of Zn and Cu with it. With an increase in the Cu and Zn content, the amount of WSOM extracted with cold water increases due to rise in the complex-bound metal compounds associated with it. The content of complex-bound compounds Zn in Spolic Technosols reaches 50% of the total metal content. It is shown that one of the biogeochemical mechanisms of microorganisms' adaptation to metal contamination is clearly manifested by the increase in the content of WSOM. The precipitation of metal carbonates develops in the soil which reduces the mobility and toxicity of PTE. Due to this mechanism, a decrease in the activity of dehydrogenases and urease was not prominent in all studied soils, despite the very high level of pollution and the transformation of organic matter. The study of the relationship of PTE with the most easily transformed part of WSOM and the activity of soil enzymes is of great importance for an objective assessment of possible environmental risks.

Production of 2-keto-L-gulonic acid by metabolically engineered Escherichia coli

The 2-keto-L-gulonic acid (2-KLG) is the direct precursor for industrial vitamin C production. The main biosynthetic method for 2-KLG production is the classical two-step fermentation route. However, disadvantages of this method are emerging, including high consumption of energy, difficulties in strain screening, complex operation, and poor stability. In this study, five recombinant Escherichia coli strains overexpressing different sorbose/sorbosone dehydrogenases were constructed and used for 2-KLG production. By optimizing catalytic conditions and further expressing pyrroloquinoline quinone in the recombinant strain, the titer of 2-KLG reached 72.4 g/L, with a conversion ratio from L-sorbose of 71.2% in a 5-L bioreactor. To achieve direct biosynthesis of 2-KLG from D-sorbitol, a co-culture system consisting of Gluconobacter oxydans and recombinant E. coli was designed. With this co-culture system, 16.8 g/L of 2-KLG was harvested, with a conversion ratio from D-sorbitol of 33.6%. The approaches developed here provide alternative routes for the efficient biosynthesis of 2-KLG.

Ethanol tolerance assessment in recombinant E. coli of ethanol responsive genes from Lactobacillus buchneri NRRL B-30929

We previously identified specific proteins associated with ethanol stress response in a Lactobacillus buchneri strain capable of growing in 10% ethanol. In the current study, the exceptional roles of ethanol responsive genes are examined to determine if they can increase ethanol tolerance in E. coli host cells. The recombinant strains carrying ethanol responsive genes were subjected to growth analyses in media with and without 4% ethanol. Among the expression of these genes and growth analyses of the recombinant strains in ethanol, six genes Lbuc_0522 (NADPH-dependent methylglyoxal reductase), Lbuc_0354 (succinate semialdehyde dehydrogenase), Lbuc_1211(threonyl_tRNA synthetase), Lbuc_2051 (nitroreductase), Lbuc_0707 (branched chain amino acid aminotransferase) and Lbuc_1852 (proline-specific peptidase) conferred host cells tolerance to 4% ethanol. Six genes Lbuc_1523 (phage major capsid protein, HK 97 family), Lbuc_1319 (phosphoglycerate kinase), Lbuc_0787 encoding fumarylacetoacetate hydrolase, Lbuc_1219 encoding UDP-N-acetylmuramate-L-alanine ligase, Lbuc_0466 encoding ornithine carbamoyltransferase and Lbuc_0858 encoding glycine hydroxymethyltransferase showed no impact on growth in media with 4% ethanol with IPTG induction when compared with E. coli carrying control pET28b plasmid. The expression of two genes Lbuc_1557 (S-layer glycoprotein) and Lbuc_2157 (6-phosphogluconate dehydrogenase) resulted ethanol sensitivity phenotype.

Pediatric non-alcoholic fatty liver disease and kidney function: Effect of HSD17B13 variant

BACKGROUND

Growing evidence supports a genetic link between non-alcoholic fatty liver disease (NAFLD) and chronic kidney disease (CKD). Interesting data demonstrated that both the major NAFLD risk polymorphisms such as the I148M polymorphism in the patatin like phospholipase containing domain 3 (PNPLA3) and the E167K allele in the transmembrane 6 superfamily member 2 gene (TM6SF2) affect renal function. Recently the hydroxysteroid 17-beta dehydrogenase 13 (HSD17B13) gene has been recognized as a novel genetic variant involved in NAFLD pathophysiology. In particular, it has been showed the protective effect of the rs72613567:TA variant of this gene against liver damage both in adults and children.

AIM

To investigate the impact of the rs72613567:TA variant of the HSD17B13 gene on estimated glomerular filtration rate (eGFR) in obese children.

METHODS

We enrolled 684 obese children (mean age 10.56 ± 2.94 years; mean BMI-SDS 2.98 ± 0.78) consecutively attending our Obesity Clinic. All the patients underwent a careful clinical assessment and a comprehensive biochemical evaluation. To detect hepatic steatosis, a liver ultrasound was performed. NAFLD was defined by ultrasound detected liver steatosis and/or alanine aminotransferase (ALT) levels > 40 IU/L. The study population was divided on the basis of the NAFLD presence. Genotyping for the rs72613567:TA variant of the HSD17B13 gene in all the enrolled subjects was also made.

RESULTS

Patients carrying the HSD17B13 rare A allele showed higher eGFR levels compared with homozygous patients both among subjects with and without NAFLD. A general linear model confirmed a direct and significant association of eGFR values with HSD17B13 genotype independently of PNPLA3 and TM6SF2 polymorphisms both in patients with and without NAFLD. A comparison of regression line confirmed the influence of HSD17B13 genotype on the relationship between eGFR and age both among patients with and without NAFLD. Homozygous patients for HSD17B13 genotype with NAFLD showed a significantly higher decline of eGFR with the increase of the age compared with the patients with NAFLD carrying the HSD17B13 rare A allele (P value for intercepts = 0.005; P value for slopes = 0.94). The same effect was observed among patients without NAFLD (P value for intercepts = 0.0012; P value for slopes = 0.87).

CONCLUSION

Carriers of the HSD17B13 rare A allele showed higher eGFR levels than homozygous subjects both among subjects with and without NAFLD and independently of PNPLA3 I148M and TM6SF6 E167K polymorphisms.

Vermicomposting of invasive weed Ageratum conyzoids: Assessment of nutrient mineralization, enzymatic activities, and microbial properties

Ageratum conyzoids biomass was vermicomposted with cow dung in 25 (T₂₅), 50 (T₅₀), and 75 (T₇₅) % (v/v) ratios and changes in physicochemical characteristics, enzymatic activities (proteases, dehydrogenases, β-galactosidase and phosphatases), and microbial population (bacterial, fungal, and actinomycetes) was recorded. Vermicomposting caused a decrease in pH, OC_total (27.3-35.3%), but an increase in N_total (59.6-69.9%), P_aval (53.8-148.7%), K_total (32.2-92.43%), and Ca_total (25.5-55.3%). The peaked enzymatic activities were recorded between 5 and 15 d. T₅₀ and T₇₅ showed the highest fold increase in bacteria (2.09-to-2.51), fungi (1.48-to-2.41), actinomycetes (1.52-to-1.79) population. The maximum biomass (883.67-1480 mg), cocoon production (85.33-145.33), and population build-up in earthworm were recorded in setups with a high content of Ageratum. Germination index (>80%) and soil respiration rate suggested the non-toxic impact of vermicomposted Ageratum. Results indicate that Ageratum could be biotransformed into toxic-free manure through vermitechnology.

Sludge Amendment Affect the Persistence, Carbon Mineralization and Enzyme Activity of Atrazine and Bifenthrin

Atrazine and bifenthrin persistence study was carried out in three sludge amended soil under laboratory condition. Atrazine persisted shorter in sludge amended soil sludge-3 (half-life 23.4 days) followed by sludge-2 (half-life 30.1 days) and sludge-1 (half-life 37.1 days) than unamended control (half-life 150.5 days). Bifenthrin followed the similar pattern with sludge-3 (half-life 43.1 days) which increased to 50.3, 60.2 and 75.2 days, respectively in sludge-2, sludge-1 and unamended control representing an immense influence of sludges on degradation. Duncan's Multiple Range Test revealed that carbon mineralization process was significantly influenced by all the sludges (p < 0.0001). Sludge-3 indicated highest C_min (initial 118.16 to final 133.64 mg CO₂-C/kg) in bifenthrin and 129.91 mg CO₂-C/kg in atrazine. The relatively high C_min rate in sludge amended soil than unamended control suggested a lower persistency of both the pesticides and thus decreasing its potential ecological risk. Sludge-3 sludge amended soil increased the dehydrogenase enzyme activity as compared to sludge-1 and sludge-2 sludge in atrazine.

Remediation of PBDEs-metal co-contaminated soil by the combination of metal stabilization, persulfate oxidation and bioremediation

Laboratory experiments were performed to investigate the efficiency of a simultaneous metal stabilization, persulfate oxidation and bioremediation for decontaminating polybrominated diphenyl ethers (PBDEs) and toxic metals from an actual soil polluted by the recycling activity of electronic waste. Biochar and bentonite were applied to the soil for immobilizing heavy metals (Cu, Pb, Zn and Ni). It was found that the toxicity level declined most significantly in the case of 20 g/kg biochar +20 g/kg bentonite. A low dose of persulfate (20 mmol/kg soil) was found to be suitable for oxidizing soil PBDEs and enhancing the bioavailability of PBDEs residue. Persulfate oxidation reduced the soil organic matter content, and caused dramatic decrease of bacterial density. Nevertheless, microbial activity and number recovered on the whole during 90 days of bioremediation. Finally, a degradation efficiency of 94.6% and a mineralization efficiency of 60.3% were obtained by the hybrid treatment scheme. The pyrosequencing analysis indicates that soil bacterial community changed obviously during the treatments, and there was an enrichment of PBDE-degrading populations during bioremediation relative to that of oxidized soil.

Characterization and Application of a Robust Glucose Dehydrogenase from Paenibacillus pini for Cofactor Regeneration in Biocatalysis

Glucose dehydrogenases are important auxiliary enzymes in biocatalysis, employed in the regeneration of reduced nicotinamide cofactors for oxidoreductase catalysed reactions. Here we report the identification and characterization of a novel glucose-1-dehydrogenase (GDH) from Paenibacillus pini that prefers NAD⁺ as cofactor over NADP⁺. The purified recombinant P. pini GDH displayed a specific activity of 247.5 U/mg. The enzyme was stable in the pH range 4-8.5 and exhibited excellent thermostability till 50 °C for 24 h, even in the absence of NaCl or glycerol. Paenibacillus pini GDH was also tolerant to organic solvents, demonstrating its potential for recycling cofactors for biotransformation. The potential application of the enzyme was evaluated by coupling with a NAD⁺-dependent alcohol dehydrogenase for the reduction of acetophenone and ethyl-4-chloro-3-oxo-butanoate. Conversions higher than 95% were achieved within 2 h with low enzyme loading using lyophilized cell lysate, suggesting that P. pini GDH could be highly effective for recycling NADH in redox biocatalysis.

Soluble expression, purification and biochemical characterization of a C-7 cholesterol dehydrogenase from Drosophila melanogaster

The C-7 cholesterol dehydrogenase (NVD), which converts cholesterol to 7-dehydrocholesterol (7-DHC) by 7,8-dehydrogenation, plays a pivotal role in the metabolism of cholesterol and steroid intermediates. The NVD protein was successfully expressed in insect Sf9 cells. To reduce the production cost for industrial application, the NVD gene was cloned into E. coli BL21(DE3). However, the His-tagged NVD protein showed poor binding to Ni-NTA resin, mainly due to the formation of inclusion bodies. Consequently, the expression and solubility of NVD were optimized by respectively fusing it with maltose-binding protein (MBP), glutathione S-transferase (GST), and the nonspecific DNA binding protein from Sulfolobus solfataricus (Sso7d) as solubility tags. The NVD fusion with MBP at the N-terminus and His-tag at the C-terminus achieved a high yield of the soluble enzyme. It was further purified by ion-exchange chromatography with 95.4% purity and with a 10.4% yield. The product 7-DHC, which is produced in a reaction catalyzed by NVD and ferredoxin reductase KshB, was initially identified by GC-MS. An analysis of the amino acid sequence alignment revealed a distinct Rieske-type iron-sulfur cluster and non-heme Fe²⁺-binding domain, which are evolutionarily conserved among NVD family enzymes.

Efficient biosynthesis of 2-keto-D-gluconic acid by fed-batch culture of metabolically engineered Gluconobacter japonicus

2-keto-d-gluconic acid (2-KGA) is a key precursor for synthesising vitamin C and isovitamin C. However, phage contamination is as constant problem in industrial production of 2-KGA using Pseudomonas fluorescens. Gluconobacter holds promise for producing 2-KGA due to impressive resistance to hypertonicity and acids, and high utilisation of glucose. In this study, the 2-KGA synthesis pathway was regulated to enhance production of 2-KGA and reduce accumulation of the by-products 5-keto-d-gluconic acid (5-KGA) and d-gluconic acid (D-GA) in the 2-KGA producer Gluconobacter japonicus CGMCC 1.49. Knocking out the ga5dh-1 gene from a competitive pathway and overexpressing the ga2dh-A gene from the 2-KGA synthesis pathway via homologous recombination increased the titre of 2-KGA by 63.81% in shake flasks. Additionally, accumulation of 5-KGA was decreased by 63.52% with the resulting G. japonicas-Δga5dh-1-ga2dh-A strain. Using an intermittent fed-batch mode in a 3 L fermenter, 2-KGA reached 235.3 g L⁻¹ with a 91.1% glucose conversion rate. Scaling up in a 15 L fermenter led to stable 2-KGA titre with productivity of 2.99 g L⁻¹ h⁻¹, 11.99% higher than in the 3 L fermenter, and D-GA and 5-KGA by-products were completely converted to 2-KGA.

Microbial community activity in response to multiple contaminant exposure: a feasible tool for sediment quality assessment

Sediments represent complex mixtures and the impacts of their physical and chemical processes on biota are important for assessing potential health risks. We aimed to rank sediment samples from Guanabara Bay by developing an algorithm (quality ratio-QR), focusing on key sediment parameters (fine grain size, total organic carbon (TOC), metal concentrations) and enzymatic activities (dehydrogenase (DHA-energy production into cell) and esterases (EST-hydrolase organic matter outside the cell membrane)) of in situ microbial communities. Our QR is supported by quantitative information and significant correlations between geochemical and microbial processes. The QR is a function of the dependent term DHA/EST and the geochemical term (TOC×∑CF)/fine-grained sediment, where ∑CF is the sum of contamination factors (ratio between actual and background metal concentrations). We could rank our sampling sites into three risk classes based on QR: low, medium, and high. Our findings suggest altered homeostasis due to the development of contamination resistance. We applied a sensitivity analysis, using Brazilian law for sediment quality assessment, to calibrate our risk index. Our QR is suitable for measuring the potential health risk of any sediment, especially in developing countries with serious technical limitations, since its evaluated parameters are cheap, fast, and easy to obtain.

Using enzyme activities and soil microbial diversity to understand the effects of fluoxastrobin on microorganisms in fluvo-aquic soil

Whether now or in the foreseeable future, agricultural production cannot do without chemical pesticides. Strobilurin fungicides, including mitochondrial inhibitors, can easily enter the soil environment and causing pollution. Fluoxastrobin is one of the top-selling strobilurin fungicides. Limited information can be found in the literature on the environmental toxicity of fluoxastrobin in soil. It is essential to understand the effects of fluoxastrobin on microorganisms in fluvo-aquic soil. The present study used a Biolog-EcoPlate method to analyze the effects of fluoxastrobin on soil microbial diversity in groups exposed to 0.1, 1.0, and 2.5 mg/kg fluoxastrobin and in control groups at exposure and on days 7, 14, 21, 28, and 48. The effects of fluoxastrobin on enzyme activities (β-glucosidase, dehydrogenase, and urease) in the soil were also evaluated. The results indicated that the three tested enzyme activities were lower at each dose to a varying degree than those of the controls. The soil microbial diversity was shown to be affected according to the results of average well color development (AWCD) experiments. The present study aimed to assess environmental risks to terrestrial ecosystems under the stress of pesticide use. These results also enrich the basic data on fungicide toxicity to the soil environment and have a guiding significance for the rational use of pesticides and the sustainable utilization of resources.

Bioremediation of petroleum-contaminated soil enhanced by aged refuse

In this study, the effect of aged refuse on biodegradation of total petroleum hydrocarbons (TPH), microbial counts, soil ecotoxicity, dehydrogenase activity and microbial community compositions were investigated in solid phase reactors during a 30-week period. The results demonstrate that the removal efficiency of TPH was significantly higher in the soil supplemented with aged refuse than in the soil without aged refuse. After 30 weeks, the removal efficiencies of TPH in soils were 29.3%, 82.1%, 63.7% and 90.2% in the cases of natural attenuation, nutrient addition (with NH₄NO₃ and K₂HPO₄), supplement with 20% (w/w, dry weight basis) of aged refuse and the combination of nutrient and aged refuse. Nutrient plus aged refuse made the TPH concentration decrease to below the threshold level of commercial use required for Chinese soil quality for TPH (<3000 mg/kg) in 30 weeks. It was also found that dehydrogenase activity, bacterial counts and degrader abundance in the soil were remarkably enhanced by the addition of aged refuse (20%,w/w). Total organic carbon analysis demonstrates that large amounts of hydrocarbon intermediates occurred in the soil after bioremediation.

FabG: from a core to circumstantial catalyst

Core biochemical pathways such as Fatty-acid synthesis II (FAS II) is ascribed to the synthesis of fatty-acids, biotin and lipoic acid in prokaryotes. It has two dehydrogenases namely, FabG and FabI which interact with the fatty-acid chain bound to Acyl-carrier protein (ACP), a well-studied enzyme which binds to substrates of varying lengths. This protein-protein interaction 'broadens' the active site of these dehydrogenases thus, contributing to their flexible nature. This property is exploited for catalysing numerous chiral synthons, alkanes, long-chain alcohols and secondary metabolites in industries especially with FabG. FASI relegates FASII in eukaryotes making it a 'relic gene pool' and an antibacterial drug target with diverse inhibitor and substrate markush. FabG often substitutes other dehydrogenases for producing secondary metabolites in nature. This redundancy is probably due to gene duplication or addition events possibly making FabG, a progenitor to some of the complex short-chain dehydrogenases used in organisms and industries today.

Responses of soil enzymatic activities to transgenic Bacillus thuringiensis (Bt) crops - A global meta-analysis

Transgenic Bacillus thuringiensis (Bt) crops have been widely planted, and the resulting environmental risks have attracted extensive attention. To foresee the impacts of Bt crops on soil quality, it is essential to understand how Bt crops alter the soil enzymatic activities and what the important influencing factors are. We compiled data from 41 published papers that studied soil enzymatic activities with Bt crops and their non-Bt counterparts. The results showed that dehydrogenase and urease significantly increased, but neutral phosphatase significantly decreased under Bt crop cultivations without Bt residues incorporation. The activities of dehydrogenase, β-glucosidase, urease, nitrate reductase, alkaline phosphatase, and aryl sulfatase significantly increased under Bt crop cultivation with Bt residues incorporation. The response ratios of other enzymes were not significantly changed. Generally, the response ratios of soil enzymes were greater with Bt residues incorporation than those of Bt crop cultivations without Bt residues incorporation. Further, the response ratios of soil enzymes varied with Bt crop types and growth periods. It was the strongest under Bt cotton among Bt crops, and the significant responses usually appeared in the middle growth stages. The responses of soil enzymes ascribed more to the properties of Bt crops than to soil properties across sites. Given - significant responses of some soil enzymes to Bt crops, we recommended that soil environmental risks should be carefully evaluated over the transgenic crops.

Improved heterologous expression of the membrane-bound quinoprotein quinate dehydrogenase from Gluconobacter oxydans

Gluconobacter oxydans produces 3-dehydroquinate by oxidation of quinate through a reaction catalyzed by the quinate dehydrogenase (QDH), membrane-bound, pyrroloquinoline quinone (PQQ)-dependent dehydrogenase. We previously reported the nucleotide and deduced amino acid sequence of QDH and constructed a heterologous expression system of QDH in Pseudomonas sp. (A.S. Vangnai, W. Promden, W. De-Eknamkul, K. Matsushita, H. Toyama, Biochemistry (Moscow) 75:452-459, 2010). Through this study, we aim to update the sequences of QDH and improve the heterologous expression of QDH in Gluconobacter strains using a broad-host-range plasmid. Expression of QDH using a plasmid containing a long 5'-UTR was higher than that using a plasmid with a short 5'-UTR. In addition, the usage of the putative promoter region of the membrane-bound, alcohol dehydrogenase (ADH) of Gluconobacter resulted in higher expression levels compared to the usage of the lacZ promoter. Base substitution experiments allowed to identify the correct TTG initiation codon between two possibilities, and the result of these experiments were consistent with the N-terminal amino acid sequence of the expressed QDH. However, change of the TTG codon to ATG did not increase QDH expression. Therefore, the optimal plasmid for QDH expression included the structural gene with a long 5'-UTR and the ADH promoter. Cell membrane of the recombinant Gluconobacter strain presented approximately 10-times higher specific QDH activity than that observed in the wild-type strain.

Evolution of Dihydropyrimidine Dehydrogenase Diagnostic Testing in a Single Center during an 8-Year Period of Time

Objective

Fluoropyrimidine treatment can be optimized based on dihydropyrimidine dehydrogenase (DPD) activity. DPD dysfunction leads to increased exposure to active metabolites, which can result in severe or even fatal toxicity.

Methods

We provide an overview of 8 years of DPD diagnostic testing (n = 1194).

Results

Within the study period, our diagnostic test evolved from a single-enzyme measurement using first a radiochemical and then a nonradiochemical assay by ultra HPLC-MS in peripheral blood mononuclear cells with uracil, to a combined enzymatic and genetic test (ie, polymerase chain reaction) followed by Sanger sequence analysis of 4 variants of the DPYD gene (ie, DPYD*2A, DPYD*13, c.2846A>T, and 1129-5923C>G; allele frequencies 0.58%, 0.03%, 0.29%, and 1.35%, respectively). Patients who have 1 of the 4 variants tested (n = 814) have lower enzyme activity than the overall patient group. The majority of patients with the DPYD*2A variant (83%) consistently showed decreased enzyme activity. Only 24 (25.3%) of 95 patients (tested for 4 variants) with low enzyme activity carried a variant. Complete DPYD sequencing in a subgroup with low enzyme activity and without DPYD*2A variant (n = 47) revealed 10 genetic variants, of which 4 have not been described previously. We did not observe a strong link between DPYD genotype and enzyme activity.

Conclusions

Previous studies have shown that DPD status should be determined before treatment with fluoropyrimidine agents to prevent unnecessary side effects with possible fatal consequences. Our study in combination with literature shows that there is a discrepancy between the DPD enzyme activity and the presence of clinically relevant single nucleotide polymorphisms. At this moment, a combination of a genetic and enzyme test is preferable for diagnostic testing. (Curr Ther Res Clin Exp. 2018; 79:XXX–XXX).

Engineering of 3-ketosteroid-∆1-dehydrogenase based site-directed saturation mutagenesis for efficient biotransformation of steroidal substrates

Background

Biosynthesis of steroidal drugs is of great benefit in pharmaceutical manufacturing as the process involves efficient enzymatic catalysis at ambient temperature and atmospheric pressure compared to chemical synthesis. 3-ketosteroid-∆¹-dehydrogenase from Arthrobacter simplex (KsdD3) catalyzes 1,2-desaturation of steroidal substrates with FAD as a cofactor.

Results

Recombinant KsdD3 exhibited organic solvent tolerance. W117, F296, W299, et al., which were located in substrate-binding cavity, were predicted to form hydrophobic interaction with the substrate. Structure-based site-directed saturation mutagenesis of KsdD3 was performed with W299 mutants, which resulted in improved catalytic activities toward various steroidal substrates. W299A showed the highest increase in catalytic efficiency (k_cat/K_m) compared with the wild-type enzyme. Homology modelling revealed that the mutants enlarged the active site cavity and relieved the steric interference facilitating recognition of C17 hydroxyl/carbonyl steroidal substrates. Steered molecular dynamics simulations revealed that W299A/G decreased the potential energy barrier of association of substrates and dissociation of the corresponding products. The biotransformation of AD with enzymatic catalysis and resting cells harbouring KsdD3 WT/mutants revealed that W299A catalyzed the maximum ADD yields of 71 and 95% by enzymatic catalysis and resting cell conversion respectively, compared with the wild type (38 and 75%, respectively).

Conclusions

The successful rational design of functional KsdD3 greatly advanced our understanding of KsdD family enzymes. Structure-based site-directed saturation mutagenesis and biochemical data were used to design KsdD3 mutants with a higher catalytic activity and broader selectivity.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-0981-0) contains supplementary material, which is available to authorized users.

Isolation and characterization of the cotinine-degrading bacterium Nocardioides sp. Strain JQ2195

Cotinine, the primary nicotine metabolite, not only more stable and more difficult to degrade in the environment but is a potential health risk to human. To date, little is known about the biodegradation process of cotinine. In this study, a bacterial strain JQ2195 was isolated from municipal wastewater and was identified as Nocardioides sp. based on morphological, physiological characteristics, and 16 S rRNA gene phylogenetic analysis. This strain utilized cotinine as a sole carbon source and degraded 0.5 g L^-1 cotinine completely within 32 h. Optimum degradation of cotinine by JQ2195 was at 30 °C and pH 7.0. Two cotinine degradation intermediates were identified as 6-hydroxy-cotinine and 6-hydroxy-3-succinoylpyridine by UV/VIS spectroscopy and liquid chromatography coupled with time-of-flight mass spectrometry. In addition, about half of cotinine was transformed to 6-hydroxy-3-succinoylpyridine which was a value-added compound for biocatalysis. When 2,6-dichlorophenolindophenol was used as an electron acceptor, the cell-free extract containing the inducible cotinine dehydrogenase could convert cotinine into 6-hydroxy-cotinine with the activity 40 ± 6 mUnmg^-1.

Bioremediation of PAH-contaminated farmland: field experiment

The agricultural soil contaminated by polycyclic aromatic hydrocarbons (PAHs) is gradually emerging and becoming serious in China with the rapid development of economy. To reduce the risk of PAHs in agricultural soil and guarantee the food safety, the biological agent that Mycobacterium gilvum immobilized on modified peanut shell powder enhanced remediation of polycyclic aromatic hydrocarbon-contaminated vegetable farmland was investigated under the conditions of the field experiment. The results indicated that adding biological agent could promote PAH degradation in the soil, especially high-ring PAHs. The degradation rates of PAHs in the soil could be further improved to 16.5-43.5 %, respectively, compared with the soil without the biological agent. Adding the biological agent could significantly improve soil dehydrogenase activity and microbial diversity. It also could reduce the enrichment of PAHs in mustard planted in the polluted field, which indicated that the biological treatments might be less ecological risk. The work suggested that adding the biological agent might be a promising in situ bioremediation strategy for PAH-contaminated farmland field.

The effects of storage time and temperature on the stability of salivary phosphatases, transaminases and dehydrogenase

OBJECTIVES

To investigate the influence of temperature and storage time on salivary acid phosphatase (ACP), tartrate-resistant acid phosphatase (TRAP), alkaline phosphatase (ALP), aspartate aminotransferase (AST) and alanine aminotransferase (ALT) and lactate dehydrogenase (LDH).

DESIGN

Unstimulated whole expectorated saliva was collected from healthy men and women subjects (n=26) between 8 and 10a.m. The saliva samples were centrifuged, and the supernatants were measured for ACP, TRAP, ALP, AST, ALT and LDH activities immediately (without freezing) [baseline values] and after time intervals of 3, 7, 14 and 28days (d) of storage at -20°C and -80°C using spectrophotometric methods The influence of storage time was analyzed by one-way ANOVA followed by the Dunnett post-test, while the paired Student's-t-test was used to compare the differences between the temperature (p<0.05).

RESULTS

There was significant decline in the activities of all enzymes at -20°C with increasing storage time. This decrease was relevant from day 14 onward for the majority of the enzymes, with the exception of AST. After day 28, the more sensitive enzymes were ALP and LDH, which showed residual activity of 39% and 16%, respectively, compared with baseline values. There were considerable, but insignificant changes, in the activities of all enzymes after storage at -80°C for 28days.

CONCLUSIONS

Frozen samples should be kept at -80°C to preserve these activities, but there are restrictions for the enzymes ALP, ALT and LDH. Storage of samples at -20°C could introduce high error variance in measured activities.

Novel patient missense mutations in the HSD17B10 gene affect dehydrogenase and mitochondrial tRNA modification functions of the encoded protein

MRPP2 (also known as HSD10/SDR5C1) is a multifunctional protein that harbours both catalytic and non-catalytic functions. The protein belongs to the short-chain dehydrogenase/reductases (SDR) family and is involved in the catabolism of isoleucine in vivo and steroid metabolism in vitro. MRPP2 also moonlights in a complex with the MRPP1 (also known as TRMT10C) protein for N1-methylation of purines at position 9 of mitochondrial tRNA, and in a complex with MRPP1 and MRPP3 (also known as PRORP) proteins for 5'-end processing of mitochondrial precursor tRNA. Inherited mutations in the HSD17B10 gene encoding MRPP2 protein lead to a childhood disorder characterised by progressive neurodegeneration, cardiomyopathy or both. Here we report two patients with novel missense mutations in the HSD17B10 gene (c.34G>C and c.526G>A), resulting in the p.V12L and p.V176M substitutions. Val12 and Val176 are highly conserved residues located at different regions of the MRPP2 structure. Recombinant mutant proteins were expressed and characterised biochemically to investigate their effects towards the functions of MRPP2 and associated complexes in vitro. Both mutant proteins showed significant reduction in the dehydrogenase, methyltransferase and tRNA processing activities compared to wildtype, associated with reduced stability for protein with p.V12L, whereas the protein carrying p.V176M showed impaired kinetics and complex formation. This study therefore identified two distinctive molecular mechanisms to explain the biochemical defects for the novel missense patient mutations.

Effect of magnetite powder on anaerobic co-digestion of pig manure and wheat straw

This study investigated the effects of different amounts of magnetite powder (i.e., 0g, 1.5g, 3g, 4.5g, 6g) on the anaerobic co-digestion of pig manure (PM) and wheat straw (WS). The variations in pH, alkalinity, cellulase activity (CEA), dehydrogenase activity (DHA) and methane production, were analyzed by phases. Correlation of the activities of the two enzymes with methane production was also analyzed, and the Gompertz model was used to evaluate the efficiency of anaerobic digestion (AD) with the addition of magnetite powder. The results showed that magnetite powder had significant effects on the anaerobic co-digestion of PM and WS. The maximum total methane production with the addition of 3g of magnetite powder was 195mL/g total solids (TS), an increase of 72.1%. The CEA and DHA increased with magnetite powder in the ranges of 1.5-4.5g, 1.5-6g, respectively, while the methane production showed a better correlation with DHA than with CEA. Using the Gompertz model, the efficiency of AD was optimal when adding 3g magnetite powder, with higher methane production potential (206mL/g TS), shorter lag-phase time (14.9d) and shorter AD period (44d).

Dissipation of S-metolachlor in plant and soil and effect on enzymatic activities

The present study aimed at evaluating the dissipation of S-metolachlor (S-MET) at three doses in maize growing on diverse physico-chemical properties of soil. The effect of herbicide on dehydrogenase (DHA) and acid phosphatase (ACP) activity was estimated. A modified QuEChERS method using LC-MS/MS has been developed. The limit of quantification (0.001 mg kg^-1) and detection (0.0005 mg kg^-1) were very low for soil and maize samples. The mean recoveries and RSDs for the six spiked levels (0.001-0.5 mg kg^-1) were 91.3 and 5.8%. The biggest differences in concentration of S-MET in maize were observed between the 28th and 63rd days. The dissipation of S-MET in the alkaline soil was the slowest between the 2nd and 7th days, and in the acidic soil between the 5th and 11th days. DT₅₀ of S-MET calculated according to the first-order kinetics model was 11.1-14.7 days (soil) and 9.6-13.9 days (maize). The enzymatic activity of soil was higher in the acidic environment. One observed the significant positive correlation of ACP with pH of soil and contents of potassium and magnesium and negative with contents of phosphorus and organic carbon. The results indicated that at harvest time, the residues of S-MET in maize were well below the safety limit for maize. The findings of this study will foster the research on main parameters influencing the dissipation in maize ecosystems.

DHRS7 (SDR34C1) - A new player in the regulation of androgen receptor function by inactivation of 5α-dihydrotestosterone?

DHRS7 (SDR34C1) has been associated with potential tumor suppressor effects in prostate cancer; however, its function remains largely unknown. Recent experiments using purified recombinant human DHRS7 suggested several potential substrates, including the steroids cortisone and Δ4-androstene-3,17-dione (androstenedione). However, the substrate and cofactor concentrations used in these experiments were very high and the physiological relevance of these observations needed to be further investigated. In the present study, recombinant human DHRS7 was expressed in intact HEK-293 cells in order to investigate whether glucocorticoids and androgens serve as substrates at sub-micromolar concentrations and at physiological cofactor concentrations. Furthermore, the membrane topology of DHRS7 was revisited using redox-sensitive green-fluorescent protein fusions in living cells. The results revealed that (1) cortisone is a substrate of DHRS7; however, it is not reduced to cortisol but to 20β-dihydrocortisone, (2) androstenedione is not a relevant substrate of DHRS7, (3) DHRS7 catalyzes the oxoreduction of 5α-dihydrotestosterone (5αDHT) to 3α-androstanediol (3αAdiol), with a suppressive effect on androgen receptor (AR) transcriptional activity, and (4) DHRS7 is anchored in the endoplasmic reticulum membrane with a cytoplasmic orientation. Together, the results show that DHRS7 is a cytoplasmic oriented enzyme exhibiting 3α/20β-hydroxysteroid dehydrogenase activity, with a possible role in the modulation of AR function. Further research needs to address the physiological relevance of DHRS7 in the inactivation of 5αDHT and AR regulation.

Kinetics of soil dehydrogenase in response to exogenous Cd toxicity

Soil dehydrogenase plays a role in the biological oxidation of soil organic matter and can be considered a good measure of the change of microbial oxidative activity under environmental pollutions. However, the kinetic characteristic of soil dehydrogenase under heavy metal stresses has not been investigated thoroughly. In this study, we characterized the kinetic characteristic of soil dehydrogenase in 14 soil types, and investigated how kinetic parameters changed under spiked with different concentrations of cadmium (Cd). The results showed that the K_m and V_max values of soil dehydrogenase was among 1.4-7.3mM and 15.9-235.2μMh^-1 in uncontaminated soils, respectively. In latosolic red soil and brown soil, the inhibitory kinetic mechanism of Cd to soil dehydrogenase was anticompetitive inhibition with inhibition constants (K_i) of 12 and 4.7mM, respectively; in other soils belonged to linear mixed inhibition, the values of K_i were between 0.7-4.2mM. Soil total organic carbon and K_i were the major factors affecting the toxicity of Cd to dehydrogenase activity. In addition, the velocity constant (k) was more sensitive to Cd contamination compared to V_max and K_m, which was established as an early indicator of gross changes in soil microbial oxidative activity caused by Cd contamination.