Recent advances in mapping environmental microbial metabolisms through 13C isotopic fingerprints

After feeding microbes with a defined ¹³C substrate, unique isotopic patterns (isotopic fingerprints) can be formed in their metabolic products. Such labelling information not only can provide novel insights into functional pathways but also can determine absolute carbon fluxes through the metabolic network via metabolic modelling approaches. This technique has been used for finding pathways that may have been mis-annotated in the past, elucidating new enzyme functions, and investigating cell metabolisms in microbial communities. In this review paper, we summarize the applications of ¹³C approaches to analyse novel cell metabolisms for the past 3 years. The isotopic fingerprints (defined as unique isotopomers useful for pathway identifications) have revealed the operations of the Entner–Doudoroff pathway, the reverse tricarboxylic acid cycle, new enzymes for biosynthesis of central metabolites, diverse respiration routes in phototrophic metabolism, co-metabolism of carbon nutrients and novel CO₂ fixation pathways. This review also discusses new isotopic methods to map carbon fluxes in global metabolisms, as well as potential factors influencing the metabolic flux quantification (e.g. metabolite channelling, the isotopic purity of ¹³C substrates and the isotopic effect). Although ¹³C labelling is not applicable to all biological systems (e.g. microbial communities), recent studies have shown that this method has a significant value in functional characterization of poorly understood micro-organisms, including species relevant for biotechnology and human health.     

Effect of a cold‐active pectinolytic system on colour development of Malbec red wines elaborated at low temperature

The effect of a new cold‐active pectinolytic system on colour of Malbec wines was studied under the following winemaking conditions: (i) fermentation at low temperature (20 °C) and (ii) prefermentative cold maceration (PCM) (5 °C–7 days) followed by traditional fermentation (28 °C). The pectinolytic system was mainly composed of polymethylgalacturonase and pectin lyase activities, detected under similar conditions to those in winemaking (pH 3.6–20 °C). The results show that the enzyme system significantly accelerated colour extraction by reducing the maceration time necessary for vinification at low temperature and shortening the PCM stage. Enzyme‐treated wines exhibited better chromatic parameters than their controls at devatting and after 6 months of storage. The cold‐active enzyme compensated the decrease in colour extraction due to the low maceration temperature, achieving high‐quality wines with chromatic characteristics similar to those of traditional wines.     

Improved microstructure and properties of the gelatin film produced through prior cross‐linking induced by horseradish peroxidase,glucose oxidase and glucose

The effects of prior enzymatic cross‐linking of bovine gelatin via horseradish peroxidase, glucose oxidase and glucose on microstructure and properties of the target film (cross‐linked gelatin film) were assessed. The cross‐linked gelatin film exhibited similar film thickness and moisture content, lower water solubility and higher opacity than the gelatin film directly prepared with bovine gelatin. The cross‐linked gelatin film also demonstrated improved thermal stability and mechanical properties, characterised by higher melting point and glass transition temperature, enhanced tensile strength and elongation at break and greater storage modulus. Prior gelatin cross‐linking resulted in 30.2% and 68.6% reductions in water vapour and CO₂ permeability of the cross‐linked gelatin film, respectively, but did not affect oil permeability. Furthermore, the cross‐linked gelatin film possessed smaller cross‐sectional voids (diameter 100?360 nm vs. 200?595 nm) than the bovine gelatin film. This study shows that cross‐linking can efficiently improve film microstructure and properties of the gelatin‐like products.     

Dose-dependent effect in the inhibition of oxidative stress and anticlastogenic potential of ginger in STZ induced diabetic rats

Ginger is an important medicinal herb has numerous bioactive components and is used in the management, control and/or treatment of diseases including diabetes mellitus. The present study was undertaken to see the dose–response effect of ginger and evaluate the possible protective effects of dietary ginger on oxidative stress and genotoxicity induced by streptozotocin (STZ) diabetic rats. Inbred male Wistar/NIN rats of 8–9 weeks old were treated with 30 mg/kg of STZ. Rats were divided into different groups of control, diabetic non-treated, and diabetic treated with ginger powder at 0.5%, 1% and 5% respectively. After feeding for a month, blood and tissues were collected to see the effect of ginger on antioxidant status, DNA damage and bone marrow genotoxicity. In this study ginger exerted a protective effect against STZ-induced diabetes by modulating antioxidant enzymes and glutathione and down regulating lipid and protein oxidation and inhibition in genotoxicity in a dose–response manner.     

Optimising by the response surface methodology the enzymatic elimination of clogging of a microfiltration membrane by pectin cake

The aim of this paper, in which clogging occurs on the filter at a constant vacuum pressure and constant pectin weight, is to find the optimal values of the variables, temperature and time, to know the best conditions to reduce this clogging by enzymatic hydrolysis. Moreover, different properties of the compression of the cake in the filter were determined such as the filtering medium total resistance (R_fT), bed porosity (ε) and the cake‐specific resistance (α) at different times and temperatures. The filter area was 0.142 m², and the value of the mass fraction of solids in the filtered suspension (S) was 0.12. Scanning electron microsopy (SEM) analyses were performed. The results showed that the compressive stress corresponding to the cake improves the flow rate in the filtration flux at the optimal temperature and time for the process, where the enzyme reaches its highest activity. The test results of this study can be applied in different system of filters during cross‐flow filtration.     

Copper(I)-Dioxygen Adducts and Copper Enzyme Mechanisms

Primary copper(I)-dioxygen (O₂) adducts, cupric-superoxide complexes, have been proposed intermediates in copper-containing dioxygen-activating monooxygenase and oxidase enzymes. Here, mechanisms of C−H activation by reactive copper-(di)oxygen intermediates are discussed, with an emphasis on cupric-superoxide species. Over the past 25 years, many synthetically derived cupric-superoxide model complexes have been reported. Due to the thermal instability of these intermediates, early studies focused on increasing their stability and obtaining physical characterization. More recently, in an effort to gain insight into the possible substrate oxidation step in some copper monooxygenases, several cupric-superoxide complexes have been used as surrogates to probe substrate scope and reaction mechanisms. These cupric superoxides are capable of oxidizing substrates containing weak O−H and C−H bonds. Mechanistic studies for some enzymes and model systems have supported an initial hydrogen-atom abstraction via the cupric-superoxide complex as the first step of substrate oxidation.     

Activity of Fluorine‐Containing Analogues of WC‐9 and Structurally Related Analogues against Two Intracellular Parasites: Trypanosoma cruzi and Toxoplasma gondii

Two obligate intracellular parasites, Trypanosoma cruzi, the agent of Chagas disease, and Toxoplasma gondii, an agent of toxoplasmosis, upregulate the mevalonate pathway of their host cells upon infection, which suggests that this host pathway could be a potential drug target. In this work, a number of compounds structurally related to WC‐9 (4‐phenoxyphenoxyethyl thiocyanate), a known squalene synthase inhibitor, were designed, synthesized, and evaluated for their effect on T. cruzi and T. gondii growth in tissue culture cells. Two fluorine‐containing derivatives, the 3‐(3‐fluorophenoxy)‐ and 3‐(4‐fluorophenoxy)phenoxyethyl thiocyanates, exhibited half‐maximal effective concentration (EC₅₀) values of 1.6 and 4.9 μm , respectively, against tachyzoites of T. gondii, whereas they showed similar potency to WC‐9 against intracellular T. cruzi (EC₅₀ values of 5.4 and 5.7 μm , respectively). In addition, 2‐[3‐ (phenoxy)phenoxyethylthio]ethyl‐1,1‐bisphosphonate, which is a hybrid inhibitor containing 3‐phenoxyphenoxy and bisphosphonate groups, has activity against T. gondii proliferation at sub‐micromolar levels (EC₅₀=0.7 μm ), which suggests a combined inhibitory effect of the two functional groups.     

Mechanisms of Enhanced Catalysis in Enzyme–DNA Nanostructures Revealed through Molecular Simulations and Experimental Analysis

Understanding and controlling the molecular interactions between enzyme substrates and DNA nanostructures has important implications in the advancement of enzyme–DNA technologies as solutions in biocatalysis. Such hybrid nanostructures can be used to create enzyme systems with enhanced catalysis by controlling the local chemical and physical environments and the spatial organization of enzymes. Here we have used molecular simulations with corresponding experiments to describe a mechanism of enhanced catalysis due to locally increased substrate concentrations. With a series of DNA nanostructures conjugated to horseradish peroxidase, we show that binding interactions between substrates and the DNA structures can increase local substrate concentrations. Increased local substrate concentrations in HRP(DNA) nanostructures resulted in 2.9‐ and 2.4‐fold decreases in the apparent Michaelis constants of tetramethylbenzidine and 4‐aminophenol, substrates of HRP with tunable binding interactions to DNA nanostructures with dissociation constants in the micromolar range. Molecular simulations and kinetic analysis also revealed that increased local substrate concentrations enhanced the rates of substrate association. Identification of the mechanism of increased local concentration of substrates in close proximity to enzymes and their active sites adds to our understanding of nanostructured biocatalysis from which we can develop guidelines for enhancing catalysis in rationally designed systems.