Enzyme reaction rates at limited water activities.
Enzyme reaction rates of dry urea and urease in controlled atmospheric water vapor pressures, determining water vapor adsorption isotherms
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Enzyme reaction rates of dry urea and urease in controlled atmospheric water vapor pressures, determining water vapor adsorption isotherms
Abstract BACKGROUND Tea is an important economic crop in China. Mulching, a modern agricultural practice, can modify the soil microenvironment and maintain the crop yield. RESULTS To investigate the effect of different mulching modes on tea plant growth, filed experiments were conducted in a Shizipu tea plantation located in Langxi Country (Xuanchen City, Anhui Province, China). Five treatments were carried out in a randomized complete block arrangement: (i) clean tillage (control); (ii) black plastic film; (iii) weed barrier fabric; (iv) rice straw mulch; and (v) intercropping with Vulpia myuros . The effects of different mulch modes on soil temperature, water moisture, soil compactness, root activity, soil enzyme activity and nutrition status on tea yield, quality and economic benefits were compared at the harvest stage. In the present study, compared with other mulch treatments, intercropping with V. myuros significantly reduced the topsoil temperature (to an optimum temperature) and soil compactness, and increased the water holding capacity in the deep soil layer, which contributed to increased tea root activity and respiration. Furthermore, intercropping with V. myuros significantly increased soil enzymes activity, soil organic matter, and the available nitrogen and phosphorus concentrations in the main root zone. Therefore, the stronger tea root activity accelerated nutrition uptake and increased the tea yield and quality‐related components of the tea, thus resulting in a larger average net income. CONCLUSION Intercropping with V. myuros could serve as a profitable agricultural method for tea production. © 2020 Society of Chemical Industry
Ionic liquids (ILs) are seen as a more sustainable alternative to volatile organic solvents that are accelerating innovations in many industries such as energy storage, separations, and bioprocessing. The ability to effectively deconstruct lignocellulosic biomass is a significant hurdle in the biorefining/bioprocessing industry and presents limitations towards the commercial production of bioproducts (such as biofuels, biomaterials, etc. ). Certain ILs have been shown to promote effective lignin removal, cellulose recovery, and sugar yields from various biomass feedstocks such as corn stover, wheat straw, sugarcane bagasse, sorghum, switchgrass, miscanthus, poplar, pine, eucalyptus, and certain mixtures of municipal solid waste. However, these improvements are often counteracted by the limited biocompatibility of ILs, which results in an IL-induced reduction in enzyme activity and stability—an important downstream step in the conversion of biomass to biofuels/bioproducts. As a result, significant efforts have been made to discover and engineer compatible enzyme-IL systems and to improve our understanding on the effect that these ILs have on these systems. This review seeks to examine the impact of ionic liquids on enzymes involved in lignocellulosic biomass deconstruction, with a specific focus on their relevance in the context of pretreatment. Beyond presenting an overview of the ionic liquid pretreatment landscape, we outline the main factors that influence enzyme activity and stability in the presence of ILs This data is consolidated and analyzed to apply this body of knowledge towards new innovations that could lead to improvements in the processing of biomass to biofuels and bioproducts.
In this study, fermentation experiments were conducted under mesophilic, thermophilic, and hyperthermophilic conditions to investigate adaptation of microbial communities and its effect on extracellular enzyme activities toward degradation of cellulose, hemicellulose and proteins in dairy manure. Here, hyperthermophilic conditions transformed the microbiome structure and stimulated activity of extracellular proteolytic, cellulolytic, and hemicellulolytic enzymes. Specifically, the activities of protease, cellulose 1,4-β-cellobiosidase, and β-glucosidase secreted by hyperthermophilic microbes were higher by 22%, 47% and 49% compared to those produced by mesophilic and thermophilic communities. Enhanced hydrolytic activity of hyperthermophilic microbes enabled improved feedstock solubilization and production of 39% and 22% more soluble COD than mesophilic and thermophilic microbes, respectively. Connections between hydrolytic function and microbial community structure at various temperatures were assessed using the PICRUSt2 computational tool. Genus Caldicoprobacter was identified as the primary candidate responsible for increased production of thermostable endo-1,4-β-glucanase, β-glucosidase and endo-1,4-β-xylanase, and enhanced hydrolytic performance of hyperthermophilic microbial community.
In C4 plants, the pyruvate (Pyr), phosphate dikinase regulatory protein (PDRP) regulates the activity of the C4 pathway enzyme Pyr, phosphate dikinase (PPDK) in a light-/dark-dependent manner. The importance of this regulatory action to C4 pathway function and overall C4 photosynthesis is unknown. To resolve this question, we assessed in vivo PPDK phospho-regulation and whole leaf photophysiology in a CRISPR–Cas9 PDRP knockout (KO) mutant of the NADP-ME C4 grass green millet (Setaria viridis). PDRP enzyme activity was undetectable in leaf extracts from PDRP KO lines. Likewise, PPDK phosphorylated at the PDRP-regulatory Thr residue was immunologically undetectable in leaf extracts. PPDK enzyme activity in rapid leaf extracts was constitutively high in the PDRP KO lines, irrespective of light or dark pretreatment of leaves. Gas exchange analysis of net CO2 assimilation revealed PDRP KO leaves had markedly slower light induction kinetics when leaves transition from dark to high-light or low-light to high-light. In the initial 30 min of the light induction phase, KO leaves had an ~15% lower net CO2 assimilation rate versus the wild-type (WT). Despite the impaired slower induction kinetics, we found growth and vigor of the KO lines to be visibly indistinguishable from the WT when grown in normal air and under standard growth chamber conditions. However, the PDRP KO plants grown under a fluctuating light regime exhibited a gradual multi-day decline in Fv/Fm, indicative of progressive photosystem II damage due to the absence of PDRP. Collectively, our results demonstrate that one of PDRP’s functions in C4 photosynthesis is to ensure optimal photosynthetic light induction kinetics during dynamic changes in incident light.
One of the primary consequences of left ventricular dysfunction (LVD) after myocardial infarction is a decrement in exercise capacity. Several factors have been hypothesized to account for this decrement, including alterations in skeletal muscle metabolism and aerobic capacity. The purpose of this study was to determine whether LVD-induced alterations in skeletal muscle enzyme activities, fiber composition, and fiber size are 1) generalized in muscles or specific to muscles composed primarily of a given fiber type and 2) related to the severity of the LVD. Female Wistar rats were divided into three groups: sham-operated controls (n = 13) and rats with moderate (n = 10) and severe (n = 7) LVD. LVD was surgically induced by ligating the left main coronary artery and resulted in elevations (P < 0.05) in left ventricular end-diastolic pressure (sham, 5 +/- 1 mmHg; moderate LVD, 11 +/- 1 mmHg; severe LVD, 25 +/- 1 mmHg). Moderate LVD decreased the activities of phosphofructokinase (PFK) and citrate synthase in one muscle composed of type IIB fibers but did not modify fiber composition or size of any muscle studied. However, severe LVD diminished the activity of enzymes involved in terminal and beta-oxidation in muscles composed primarily of type I fibers, type IIA fibers, and type IIB fibers. In addition, severe LVD induced a reduction in the activity of PFK in type IIB muscle, a 10% reduction in the percentage of type IID/X fibers, and a corresponding increase in the portion of type IIB fibers. Atrophy of type I fibers, type IIA fibers, and/or type IIB fibers occurred in soleus and plantaris muscles of rats with severe LVD. These data indicate that rats with severe LVD after myocardial infarction exhibit 1) decrements in mitochondrial enzyme activities independent of muscle fiber composition, 2) a reduction in PFK activity in type IIB muscle, 3) transformation of type IID/X to type IIB fibers, and 4) atrophy of type I, IIA, and IIB fibers.
The ability to coordinate and confine enzymes presents an opportunity to affect their performance and to create chemically active materials. Recent studies show that polymers and biopolymers can be used to scaffold enzymes, and that can lead to the modulated biocatalytic efficiency. In this work, we investigated the role of microenvironments on enzyme activity using a well-defined molecular scaffold. An enzyme, glucose oxidase (GO x ), was positioned at different locations of a three-dimensional (3D) octahedral DNA scaffold (OS), allowing the enzyme’s polyanionic environments to be altered. Using electrical sensing, based on a bipolar junction transistor, we measured directly and in real-time the enzyme’s proton generation at these different microenvironments. We found a 200% enhancement of immobilized enzyme over free GOx and about a 30% increase in catalytic rates when the enzyme was moved on the same molecular scaffold to a microenvironment with a higher local concentration of polyanions, which suggests a role of local pH on the enzymatic activity.
Phenotypic plasticity of traits is commonly measured in plants to improve understanding of organismal and ecosystem responses to climate change but is far less studied for microbes. Specifically, decomposer fungi are thought to display high levels of phenotypic plasticity and their functions have important implications for ecosystem dynamics. Assessing the phenotypic plasticity of fungal traits may therefore be important for predicting fungal community response to climate change. Here, we assess the phenotypic plasticity of 15 fungal isolates (12 species) from a Southern California grassland. Fungi were incubated on litter at five moisture levels (ranging from 4–50% water holding capacity) and at five temperatures (ranging from 4–36 °C). After incubation, fungal biomass and activities of four extracellular enzymes (cellobiohydrolase (CBH), β -glucosidase (BG), β -xylosidase (BX), and N-acetyl- β - D -glucosaminidase (NAG)) were measured. We used response surface methodology to determine how fungal phenotypic plasticity differs across the moisture-temperature gradient. We hypothesized that fungal biomass and extracellular enzyme activities would vary with moisture and temperature and that the shape of the response surface would vary between fungal isolates. We further hypothesized that more closely related fungi would show more similar response surfaces across the moisture-temperature gradient. In support of our hypotheses, we found that plasticity differed between fungi along the temperature gradient for fungal biomass and for all the extracellular enzyme activities. Plasticity also differed between fungi along the moisture gradient for BG activity. These differences appear to be caused by variation mainly at the moisture and temperature extremes. We also found that more closely related fungi had more similar extracellular enzymes activities at the highest temperature. Altogether, this evidence suggests that with global warming, fungal biodiversity may become increasingly important as functional traits tend to diverge along phylogenetic lines at higher temperatures.
ABSTRACT Development of transgenic bioenergy sorghum [ Sorghum bicolor (L.) Moench] with increased contents of mixed‐linkage (1,3;1,4)‐β‐glucan (MLG) is an important step towards enhancing quality of bioenergy feedstocks. Since MLG‐enhancement leads to greater biomass digestibility, our overarching hypothesis is that root residues of MLG‐enhanced plants may be more readily decomposed in the soil, potentially creating new opportunities for optimizing soil carbon (C) sequestration, nutrient cycling, and overall agricultural sustainability. The study examined morphological, chemical, and enzymatic characteristics of fine and coarse roots of four bioenergy sorghum genotypes. Then, we incubated the roots within soils with contrasting vegetation histories while measuring C mineralization, microbial biomass C (MBC), and activity of hydrolytic enzymes and calculating vector length and vector angle enzymatic stoichiometry parameters. The results indicated that MLG‐enhancing transformations increased root total nitrogen (N) contents, decreased C/N ratios, and were associated with higher MLG concentrations in fine than in coarse roots. Incubations with transgenic roots led to 16%–38% higher MBC and 19%–41% lower microbial metabolic quotient (qCO 2 ). While enzyme activity differed markedly among the studied genotypes, it did not directly respond to MLG levels in root tissues. The increase in MBC without concurrent increases in C mineralization or hydrolytic enzyme activities in transgenic genotypes suggests that MLG enhancement promoted microbial anabolic retention of root‐derived C rather than stimulating catabolic decomposition. Enzymatic vector results indicated that these parameters reflect a variety of drivers behind microbial enzyme production, including availability of specific substrates, such as MLG here, and/or deficiency in specific nutrients, such as phosphorus (P). The study confirms the positive impacts from the roots of engineered MLG‐enhanced bioenergy plants on soil microbial activity and highlights the interactive influences on the MLG‐enhancement effects from root size and inherent soil properties.
Abstract Heme enzymes, with the pentacoordinate heme iron active sites, possess high catalytic activity and selectivity in biosensing applications. However, they are still subject to limited catalytic stability in the complex environment and high cost for broad applications in electrochemical sensing. It is meaningful to develop a novel substitute that has a similar structure to some heme enzymes and mimics their enzyme activities. One emerging strategy is to design the Fe‐N‐C based single‐atomic site catalysts (SASCs). The obtained atomically dispersed Fe‐N x active sites can mimic the active sites of heme enzymes effectively. In this work, a SASC (Fe‐SASC/NW) is synthesized by doping single iron atoms in polypyrrole (PPy) derived carbon nanowire via a zinc‐atom‐assisted method. The proposed Fe‐SASC/NW shows high heme enzyme‐like catalytic performance for hydrogen peroxide (H 2 O 2 ) with a specific activity of 42.8 U mg −1 . An electrochemical sensor based on Fe‐SASC/NW is developed for the detection of H 2 O 2 . This sensor exhibits a wide detection concentration range from 5.0 × 10 −10 m to 0.5 m and an excellent limit of detection (LOD) of 46.35 × 10 −9 m . Such excellent catalytic activity and electrochemical sensing sensitivity are attributed to the isolated Fe‐N x active sites and their structural similarity with natural metalloproteases.
Colocalization of cascade enzymes is broadly discussed as a phenomenon that can boost the cascade reaction throughput, although a direct experimental verification is often challenging. This is mainly due to difficulties in establishing proper size regimes and in the analytical quantification of colocalization effect with adequate experimental systems and simulations. In this study, by taking advantage of reversible DNA-directed colocalization of enzymes on microspheres, we established a cascade system that can be used to directly evaluate the colocalization effect with exactly the same experimental settings except for the state of enzyme dispersion. In the regime of highly dilute microspheres of particular sizes, the colocalized cascade shows enhanced activity compared with the freely diffusing cascade, as evidenced by a shortened lag phase in the time-course production. Reaction-diffusion modeling reveals that the enhancement can be ascribed to the initial accumulation of intermediate substrate around the colocalized enzymes and is found to be carrier-size-dependent. Further, this work demonstrates the dependence of the colocalization effect of enzyme cascades on an interplay of nano-and microscales, lending theoretical support to the rational design of highly efficient multienzyme catalysts.
Transport of extracellular hydrolytic enzymes in soils has always been a subject of doubt. The considerations against its importance are that (i) enzymes benefit their producers the most when they remain in close proximity; and (ii) enzymes are large molecules with low mobility due to high affinity to fine soil particles and organic matter. However, soil mineral colloids (SMC), to which extracellular enzymes also have an affinity and which are known to facilitate transport of a broad variety of chemicals and microorganisms in soils, can serve as vehicles for enzyme transport as well. Since current literature lacks information on enzyme transport in soils, our goal was to determine whether enzymes are transported and, if so, whether they are transported in a free- or in a colloid-associated form. We conducted column transport experiments with four hydrolytic enzymes, namely, β-glucosidase, acid-phosphatase, cellobiohydrolase, and xylosidase, in soils with contrasting textures. The eluents containing enzymes were applied on top of soil columns, while enzyme activities, SMC, and electrical conductivity were measured in the effluents from the columns. Our results provided evidence of joint enzyme transport with soil colloids. The enzymes associated with the coarse SMC (1 μm < Ø) contributed 52–88% of the total enzyme activity in the effluents. The remaining enzyme activity was attributed to the enzymes associated with organic colloids, fine SMC (Ø < 1 μm) and free enzymes in solution. Furthermore, this study suggested a dual effect of ionic strength in the soil suspension on enzyme activity and their release from soils with soil colloids.
Changes in precipitation represent a major effect of climate change on tropical forests, which contain some of the earth’s largest terrestrial carbon (C) stocks. Such changes are expected to influence microbes, nutrients, and the fate of C in tropical forest soils. To explore this, we assessed soil microbial biomass, potential extracellular enzyme activities, and nutrient availability in a partial throughfall exclusion experiment in four seasonal lowland tropical humid forests in Panama with wide variation in precipitation and soil fertility. We hypothesized that throughfall exclusion would reduce microbial biomass and activity and accentuate dry season soil nutrient accumulation, with larger effects in wetter, less droughtresistant forests. We observed a baseline seasonal pattern of decreased microbial biomass and increased extractable dissolved organic C (DOC), total dissolved nitrogen (TDN), nitrate (NO 3 – ), and resinextractable phosphorus (P) in the dry season, with the strongest patterns for nitrogen (N). However, potential enzyme activities showed no consistent seasonality. In line with seasonal drying, throughfall exclusion decreased soil microbial biomass in the wet season and increased TDN and NO 3 – , especially in the dry season. In contrast to seasonal drying, throughfall exclusion decreased DOC and did not affect resinextractable P, but slightly decreased potential phosphatase activities. Potential enzyme activities varied among sites and sampling times, but did not explain much variation in microbial biomass or substrate availability. We conclude that reduced rainfall in tropical forests might accentuate some dry season patterns, like reductions in microbial biomass and accumulation of extractable nutrients. However, our data also suggest new patterns, like reduced inputs of DOC to soils with drying, which could have cascading effects on soil ecological function and C storage.
Extracellular enzyme activity is a well-established parameter for evaluating microbial biogeochemical roles in marine ecosystems. The presence and activity of extracellular enzymes in seawater provide insights into the quality and quantity of organic matter being processed by the present microorganisms. A key challenge in our understanding of these processes is to decode the extracellular enzyme repertoire and activities of natural communities at the single-cell level. Current measurements are carried out on bulk or size-fractionated samples capturing activities of mixed populations. This approach – even with size-fractionation – cannot be used to trace enzymes back to their producers, nor distinguish the active microbial members, leading to a disconnect between measured activities and the producer cells. By targeting extracellular enzymes and resolving their activities at the single-cell level, we can investigate underlying phenotypic heterogeneity among clonal or closely related organisms, characterize enzyme kinetics under varying environmental conditions, and resolve spatio-temporal distribution of individual enzyme producers within natural communities. In this perspective piece, we discuss state-of-the-art technologies in the fields of microfluidic droplets and functional screening of prokaryotic cells for measuring enzyme activity in marine seawater samples, one cell at a time. We further elaborate on how this single-cell approach can be used to address research questions that cannot be answered with current methods, as pertinent to the enzymatic degradation of organic matter by marine microorganisms.
Human skeletal muscle fibers seem to share most of the same interrelationships among myosin ATPase activity, myosin heavy chain (MHC) phenotype, mitochondrial enzyme activities, glycolytic enzyme activities, and cross-sectional area (CSA) as found in rat, cat, and other species. One difference seems to be that fast fibers with high mitochrondrial content occur less frequently in humans than in the rat or cat. Recently, we have reported that the type of MHC expressed and the size of the muscle fibers in humans that have spent 11 days in space change significantly. Specifically, about 8% more fibers express fast MHCs and all phenotypes atrophy in the vastus lateralis (VL) post compared to preflight. In the present paper we examine the relationships among the population of myonuclei, MHC type, and CSA of single human muscle fibers before and after spaceflight. These are the first data that define the relationship among the types of MHC expressed, myonuclei number, and myonuclei domain of single fibers in human muscle. We then compare these data to similar measures in the cat. In addition, the maximal torque that can be generated by the knee extensors and their fatigability before and after spaceflight are examined. These data provide some indication of the potential physiologica consequences of the muscle adaptations that occur in humans in response to spaceflight.
The overarching goal of this project was to attain fundamental understanding of structural organization, self-assembly, and function of redox-active enzymes and biological energy transduction systems localized at biological (cellular membranes) as well as manmade bio-nano interfaces. During this project we developed (1) nanopore surfaces suitable to stabilization of functional redox active enzymes and (2) experimental protocols for loading for loading of redox active enzymes into nanopores and taking advantage of self-assembly for forming layer(s) of redox active enzymes inside the nanochannels formed in anodic aluminum oxide (AAO) substrates.
Root exudation is a key process for plant nutrient acquisition, but the controls on root exudation and its relationship to soil C and N processes in agroecosystems are unclear. We hypothesized that root exudation rates would be related to root morphological traits, N fertilization, and soil moisture. We also anticipated that root exudation would be correlated with bulk soil enzyme activity. Root exudation, root traits, and bulk soil extracellular enzyme activity were assessed in maize (Zea mays L.), soybean (Glycine max (L.) Merr.), biomass sorghum (Sorghum bicolor (L.) Moench), giant miscanthus (Miscanthus × giganteus), and switchgrass (Panicum virgatum L.). Measurements were taken in situ during two growing seasons with contrasting precipitation regimes, and N fertilization rate was varied in sorghum during one year. Specific root exudation (per unit root surface area) was negatively related to root diameter and was generally higher in annuals than perennials. Sorghum N fertilization did not affect root exudation rates, and soil moisture regime had no effect on annual root exudation rates within maize, sorghum, and miscanthus. Specific root exudation was negatively related to bulk soil C- and N-degrading soil enzyme activities. Intrinsic plant characteristics appeared more important than environmental variables in controlling in situ root exudation rates. The relationships between root diameter, root exudation, and soil C and N processes link root morphological traits to soil functions and demonstrate the potential tradeoffs among plant nutrient acquisition strategies in agroecosystems.
Root exudation is a key process for plant nutrient acquisition, but the controls on root exudation and its relationship to soil C and N processes in agroecosystems are unclear. We hypothesized that root exudation rates would be related to root morphological traits, N fertilization, and soil moisture. We also anticipated that root exudation would be correlated with bulk soil enzyme activity. Root exudation, root traits, and bulk soil extracellular enzyme activity were assessed in maize (Zea mays L.), soybean (Glycine max (L.) Merr.), biomass sorghum (Sorghum bicolor (L.) Moench), giant miscanthus (Miscanthus × giganteus), and switchgrass (Panicum virgatum L.). Measurements were taken in situ during two growing seasons with contrasting precipitation regimes, and N fertilization rate was varied in sorghum during one year. Specific root exudation (per unit root surface area) was negatively related to root diameter and was generally higher in annuals than perennials. Sorghum N fertilization did not affect root exudation rates, and soil moisture regime had no effect on annual root exudation rates within maize, sorghum, and miscanthus. Specific root exudation was negatively related to bulk soil C- and N-degrading soil enzyme activities. Intrinsic plant characteristics appeared more important than environmental variables in controlling in situ root exudation rates. The relationships between root diameter, root exudation, and soil C and N processes link root morphological traits to soil functions and demonstrate the potential tradeoffs among plant nutrient acquisition strategies in agroecosystems.