Enzyme Pool Research Articles

Temperature sensitivity of extracellular enzymes differs with peat depth but not with season in an ombrotrophic bog

Peatlands contain a large portion of Earth's terrestrial soil organic matter in part due to a reduction in decomposition rates. Organic matter decomposition is initially mediated by extracellular enzyme activity, which is in turn controlled by temperature, moisture, and substrate availability; and all are subject to seasonal variation. As depth increases in peatlands, temperature variability and labile carbon inputs decrease. We hypothesized that the more stable recalcitrant subsurface would contain a smaller less diverse enzyme pool, that is better adapted to a narrow temperature range. Thus temperature dependence would be diminished at depth compared to superficial peat. Potential enzyme activity rates were determined across seasons and with depth in peat samples collected from the Marcell Experimental Forest in northern Minnesota, USA. The temperature dependence, assessed by activation energy, was quantified for three hydrolytic enzymes involved in nutrient cycling at up to 15 temperature points ranging from 2 °C to 65 °C. Potential enzyme activity decreased with peat depth as expected and corresponded with changes in peat composition and microbial biomass from the acrotelm to the catotelm. In an environmentally relevant temperature range (2–23 °C), activation energy decreased with depth for β-glucosidase as predicted and leucine amino peptidase activation energy was the lowest of all enzymes. Stable temperatures at depth appear to result in a microbial community containing enzymes that have lower sensitivity to temperature increases. Surprisingly, there was no significant seasonal effect on enzyme temperature dependence observed in our study. Based on these results, and without shifts in microbial community composition, warming of peat could result in increased carbon and phosphorus cycling at the surface but little change at depth. Additionally differences in enzyme temperature sensitivity suggest nitrogen cycling could remain constant with warming, potentially resulting in proteolytic nitrogen cycling being decoupled from carbon and phosphorus cycling.

Overcoming the expression barrier of the ferredoxin‑hydrogenase chimera in Chlamydomonas reinhardtii supports a linear increment in photosynthetic hydrogen output

While the prospect of producing hydrogen from photosynthetic microalgae has long been described as one of the promising directions towards achieving a renewable fuel source, current endeavors towards this goal face serious limitations including the inefficient electron supply to hydrogenase and the enzyme's sensitivity to molecular oxygen. In this work we express our ferredoxin‑hydrogenase (fd-hyd) fusion enzyme in a hydrogenase knockout Chlamydomonas reinhardtii mutant and compare its hydrogen production traits to those of wild-type strains. We found that the active enzyme abundance in both systems is in linear correlation with photosynthetic hydrogen production, thus establishing that protein abundance is an additional important bottleneck in the process of hydrogen photo-production. We report here the isolation of two clones with high expression of fd-hyd; OP68 and R2D2, created by either nuclear or chloroplast transformation, respectively. The study of these clones shows that fd-hyd's roughly 4.5-fold higher H2 production efficiency, compared to the native hydrogenase, is maintained in high expression regimes. By comparing a strain's active enzyme pool to its total protein amount, we observed that the engineered clones harbor a large non-mature enzyme pool, indicating that natural maturation of the fd-hyd saturates at a lower level than the native hydrogenase. Subsequently, we measured mRNA levels by quantitative PCR and observed that while the two clones express roughly the same amount of protein, R2D2 has considerably more mRNA. Thus improving transcription rates in nuclear transformants or translation efficiency in chloroplast transformants are both potential routes towards further increasing protein abundance. Finally, we show that these clones are able to continuously produce H2 in sealed bioreactors for five days, significantly outcompeting their parental wild-type strain.

Catalytic power of enzymes decreases with temperature: New insights for understanding soil C cycling and microbial ecology under warming.

Most current models of soil C dynamics predict that climate warming will accelerate soil C mineralization, resulting in a long-term CO2 release and positive feedback to global warming. However, ecosystem warming experiments show that CO2 loss from warmed soils declines to control levels within a few years. Here, we explore the temperature dependence of enzymatic conversion of polymerized soil organic C (SOC) into assimilable compounds, which is presumed the rate-limiting step of SOC mineralization. Combining literature review, modelling and enzyme assays, we studied the effect of temperature on activity of enzymes considering their thermal inactivation and catalytic activity. We defined the catalytic power of enzymes (Epower ) as the cumulative amount of degraded substrate by one unit of enzyme until its complete inactivation. We show a universal pattern of enzyme's thermodynamic properties: activation energy of catalytic activity (EAcat )<activation energy of thermal inactivation (EAinact ). By investing in stable enzymes (high EAinact ) having high catalytic activity (low EAcat ), microorganisms may maximize the Epower of their enzymes. The counterpart of such EAs' hierarchical pattern is the higher relative temperature sensitivity of enzyme inactivation than catalysis, resulting in a reduction in Epower under warming. Our findings could explain the decrease with temperature in soil enzyme pools, microbial biomass (MB) and carbon use efficiency (CUE) reported in some warming experiments and studies monitoring the seasonal variation in soil enzymes. They also suggest that a decrease in soil enzyme pools due to their faster inactivation under warming contributes to the observed attenuation of warming effect on soil C mineralization. This testable theory predicts that the ultimate response of SOC degradation to warming can be positive or negative depending on the relative temperature response of Epower and microbial production of enzymes.

The Role of Cytochromes P450 in Infection

Cytochromes are expressed in many different tissues of the human body. They are found mostly in intestinal and hepatic tissues. Cytochromes P450 (CYPs) are enzymes that oxidize substances using iron and are able to metabolize a large variety of xenobiotic substances. CYP enzymes are linked to a wide array of reactions including and O-dealkylation, S-oxidation, epoxidation, and hydroxylation. The activity of the typical P450 cytochrome is influenced by a variety of factors, such as genus, environment, disease state, herbicide, alcohol, and herbal medications. However, diet seems to play a major role. The mechanisms of action of dietary chemicals, macro- and micronutrients on specific CYP isoenzymes have been extensively studied. Dietary modulation has effects upon the metabolism of xenobiotics. Cytochromes harbor intra- or interindividual and intra- or interethnic genetic polymorphisms. Bacteria were shown to express CYP-like genes. The tremendous metabolic activity of the microbiota is associated to its abundant pool of CYP enzymes, which catalyze phase I and II reactions in drug metabolism. Disease states, intestinal disturbances, aging, environmental toxic effects, chemical exposures or nutrition modulate the microbial metabolism of a drug before absorption. A plethora of effects exhibited by most of CYP enzymes can resemble those of proinflammatory cytokines and IFNs. Moreover, they are involved in the initiation and persistence of pathologic pain by directly activating sensory neurons and inflammatory cytokines.

Two novel deep-sea sediment metagenome-derived esterases: residue 199 is the determinant of substrate specificity and preference

BackgroundThe deep-sea environment harbors a vast pool of novel enzymes. Owing to the limitations of cultivation, cultivation-independent has become an effective method for mining novel enzymes from the environment. Based on a deep-sea sediment metagenomics library, lipolytic-positive clones were obtained by activity-based screening methods.ResultsTwo novel esterases, DMWf18-543 and DMWf18-558, were obtained from a deep-sea metagenomic library through activity-based screening and high-throughput sequencing methods. These esterases shared 80.7% amino acid identity with each other and were determined to be new members of bacterial lipolytic enzyme family IV. The two enzymes showed the highest activities toward p-nitrophenyl (p-NP) butyrate at pH 7.0 and 35–40 °C and were found to be resistant to some metal ions (Ba2+, Mg2+, and Sr2+) and detergents (Triton X-100, Tween 20, and Tween 80). DMWf18-543 and DMWf18-558 exhibited distinct substrate specificities and preferences. DMWf18-543 showed a catalytic range for substrates of C2–C8, whereas DMWf18-558 presented a wider range of C2–C14. Additionally, DMWf18-543 preferred p-NP butyrate, whereas DMWf18-558 preferred both p-NP butyrate and p-NP hexanoate. To investigate the mechanism underlying the phenotypic differences between the esterases, their three-dimensional structures were compared by using homology modeling. The results suggested that residue Leu199 of DMWf18-543 shortens and blocks the substrate-binding pocket. This hypothesis was confirmed by the finding that the DMWf18-558-A199L mutant showed a similar substrate specificity profile to that of DMWf18-543.ConclusionsThis study characterized two novel homologous esterases obtained from a deep-sea sediment metagenomic library. The structural modeling and mutagenesis analysis provided insight into the determinants of their substrate specificity and preference. The characterization and mechanistic analyses of these two novel enzymes should provide a basis for further exploration of their potential biotechnological applications.

Species-specific response to acute hyperthermal stress of Haworthia (Asphodelaceae) plants

An increase in environmental temperature is one of the most common stress factors for plant organisms. The study of the plants’ adaptation to stress factors remains extremely important and relevant. This article presents the results of a acute short-term influence of hyperthermia on species of two subgenera of the genus Haworthia Duval. We investigated the different levels of antioxidant protection and damage degree of the members of two subgenera of the genus Haworthia at the biochemical level, measuring the lipid peroxidation, superoxide dismutase and peroxidase activities, total flavonoid content and content of photosynthetic pigments with a spectrophotometer. To determine the drought tolerance of plants, the water supply of tissues, water shortage and loss of water after an hour of wilting were measured. The values for different groups were compared by ANOVA followed by the Tukey multiple comparison test. The studied plants were warmed in a thermostat at temperatures of 40 °C and 50 °C for three hours under the conditions of natural light. The control group of plants was kept at 25 °C. The research has shown that H. attenuata, H. limifolia and H. cymbiformis are characterized with the increase of concentration of malonic dialdehyde at 40 °C and 50 °C, but a significant difference of values wasn’t received,which indicates the relative resistance of these plants to the influence of high temperatures. The sharp increase of temperature causes the highest level of lipid peroxidation in H. parksiana plants, along with which, warming to 50 °C launches a mechanism of activation and synthesis of superoxide dismutase and flavonoids for the plants. The studied species of the subgenus Haworthia have a photosynthetic system relatively resistant to thermal stress in comparison to the subgenus Hexangulares. H. limifolia plants have a slight inhibition of photosynthesis. The adaptation of H. cymbiformis to thermal stress is due to the strategy of accumulation of a pool of active enzymes, superoxide dismutase, peroxidase, flavonoids under normal conditions and the activation of new peroxidase enzymes as a result of stress. H. attenuata is characterized by activation of new enzymes of superoxide dismutase and peroxidase under stress. It was found that H. cymbiformis and H. attenuata are more heat resistant in comparison with the other two species. Acute short-term hyperthermia has a different influence on the antioxidant system of different species of Haworthia. H. limifolia has the highest drought tolerance, H. cymbiformis has the lowest, the other two species from different subgenera have similar drought tolerance indicators. We did not find any dependence of the mechanisms of action of the antioxidant system under hyperthermia on the type of adaptation to arid conditions at the anatomical level in plants of different subgenera of the genus Haworthia.

Optimization of endoglucanase production from Trichoderma harzianum strain HZN11 by central composite design under response surface methodology

The utilization of abundantly available lignocellulosic biomass requires an efficient cellulolytic enzyme system. Evaluation of an efficient microbial system is a crucial part for the development of useful enzyme production in an industrial process. The present study reports the production of cellulolytic enzymes from various lignocellulosic biomasses by Trichoderma harzianum strain HZN11 characterized by 18S rDNA sequencing. The organism revealed a well-balanced cellulolytic complex of enzyme production (endoglucanase 30.32 U g−1, exoglucanase 15.08 U g−1, FPase 5.56 U g−1, cellobiase 17.92 U g−1, β-glucosidase 11.21 U g−1, and xylanase 1740 U g−1) from sweet sorghum bagasse under solid-state fermentation. Statistical optimization by Plackett–Burman design constituting of 12 experimental runs at two levels of seven independent variables revealed the significant effect of four variables, namely, protease peptone, lactose, MgSO4·7H2O, and K2HPO4 on endoglucanase production at 95% confidence level with R 2=97.68%. Response surface methodology using central composite design was employed with 31 experimental runs at 5 levels with 4 significant independent variables. The responses in the form of contour and 3D plots showed significant interaction effects. Significant interactions existed between the variables at p < 0.05 with R 2=97.3%. The model generated through these designs was validated giving a 2.31-fold increase in endoglucanase production. The isolated T. harzianum strain HZN11 produced an efficient pool of cellulolytic enzymes which is essential for efficient hydrolysis of biomass. The strain HZN11 also possessed a significant capability of cellobiase production which is usually deficient in other strains. Higher yields of endoglucanase could be employed for bioethanol production.

Erythritol production by Yarrowia lipolytica from okara pretreated with the in-house enzyme pools of fungi

Okara (soybean residue) is an ideal erythritol feedstock due to its low price and high-nutrient content. Fungal-fermentations were carried out in okara using in-house enzyme pools generated by Mucor flavus or Trichoderma reesei to make okara more accessibility in the subsequent erythritol production using Yarrowia lipolytica. Mucor-fermented okara produced a high erythritol yield because of its special component and micromorphology. Five days is the optimal period for Mucor fermentation. Different fermentation modes were compared in terms of erythritol production and yield. The concentration of Mucor-fermented okara in erythritol fermentation medium was optimal at 30.0g/L. Moreover, 40.0g/L NaCl was added as the osmotic regulator. No extra ingredient was needed during this process. Results of 5-L fermentations showed that an erythritol titer of 14.7g/L, with a yield of 0.49g/g okara was obtained. These findings indicated that Mucor-fermented okara was an economically alternative feedstock for low-cost erythritol production.

Extracellular enzyme kinetics and thermodynamics along a climate gradient in southern California

Microbial decomposers produce extracellular enzymes to degrade complex plant polymers, making plant C available for metabolism and eventual respiration back to the atmosphere as CO2. Knowledge of how extracellular enzyme kinetics and microbial activity vary with climate is therefore valuable for predicting how future carbon cycling may be affected by climate change, but studies investigating such dynamics in more xeric ecosystems are underrepresented in the literature. We investigated how microbial biomass, litter chemistry, and extracellular enzymes (Vmax and Km) and their temperature sensitivities varied along a Mediterranean climate gradient in southern California. Total microbial biomass did not vary among sites along the gradient in either the dry or the wet season. In contrast, extracellular enzyme Vmax and Km varied as a function of fungal biomass and substrate availability. We also found that Vmax of most enzymes was more sensitive to temperature in colder sites than in warmer sites, though only in the dry season. In contrast, Km of multiple enzymes was more sensitive to temperature in warmer sites across both seasons. Observed enzyme Vmax and Km were indicative of extracellular enzyme accumulation in the drier sites along the gradient, which may contribute to the large pulses of respiration that follow rewetting events in these xeric systems. Variation in enzyme characteristics along the gradient indicate that as these systems become more arid in the future, enzyme dynamics will shift from smaller, potentially more active pools to larger, potentially less active enzyme pools that accumulate over dry periods. In addition, rates of enzymatic decomposition will likely be most sensitive to rising temperatures in the coldest sites along our gradient.

Substrate selectivity in the zDHHC family of S-acyltransferases.

S-acylation is a reversible lipid modification occurring on cysteine residues mediated by a family of membrane-bound 'zDHHC' enzymes. S-acylation predominantly results in anchoring of soluble proteins to membrane compartments or in the trafficking of membrane proteins to different compartments. Recent work has shown that although S-acylation of some proteins may involve very weak interactions with zDHHC enzymes, a pool of zDHHC enzymes exhibit strong and specific interactions with substrates, thereby recruiting them for S-acylation. For example, the ankyrin-repeat domains of zDHHC17 and zDHHC13 interact specifically with unstructured consensus sequences present in some proteins, thus contributing to substrate specificity of these enzymes. In addition to this new information on zDHHC enzyme protein substrate specificity, recent work has also identified marked differences in selectivity of zDHHC enzymes for acyl-CoA substrates and has started to unravel the underlying molecular basis for this lipid selectivity. This review will focus on the protein and acyl-CoA selectivity of zDHHC enzymes.

A 9-pool metabolic structured kinetic model describing days to seconds dynamics of growth and product formation by Penicillium chrysogenum.

A powerful approach for the optimization of industrial bioprocesses is to perform detailed simulations integrating large-scale computational fluid dynamics (CFD) and cellular reaction dynamics (CRD). However, complex metabolic kinetic models containing a large number of equations pose formidable challenges in CFD-CRD coupling and computation time afterward. This necessitates to formulate a relatively simple but yet representative model structure. Such a kinetic model should be able to reproduce metabolic responses for short-term (mixing time scale of tens of seconds) and long-term (fed-batch cultivation of hours/days) dynamics in industrial bioprocesses. In this paper, we used Penicillium chrysogenum as a model system and developed a metabolically structured kinetic model for growth and production. By lumping the most important intracellular metabolites in 5 pools and 4 intracellular enzyme pools, linked by 10 reactions, we succeeded in maintaining the model structure relatively simple, while providing informative insight into the state of the organism. The performance of this 9-pool model was validated with a periodic glucose feast-famine cycle experiment at the minute time scale. Comparison of this model and a reported black box model for this strain shows the necessity of employing a structured model under feast-famine conditions. This proposed model provides deeper insight into the in vivo kinetics and, most importantly, can be straightforwardly integrated into a computational fluid dynamic framework for simulating complete fermentation performance and cell population dynamics in large scale and small scale fermentors. Biotechnol. Bioeng. 2017;114: 1733-1743. © 2017 Wiley Periodicals, Inc.

Characterization of photosynthetic acclimation in Phoenix dactylifera by a modified Arrhenius equation originally developed for leaf respiration

Instantaneous temperature responses of leaf respiration and photosynthesis can be described by the same equation, to help understand acclimation of primary metabolism to altered growth temperature and water supply. We used a three-parameter, modified Arrhenius equation, originally developed for leaf respiration, to characterize A/T curves of Date Palm and acclimation to elevated growth temperature and water deprivation: $$A_{\text{T}} = A_{\text{ref}} \times e^{{\left[ {\frac{{E_{\text{o}} (\text{Ref}_{\text{A}} )}}{\Re } \times \left( {\frac{{T - T_{\text{ref}} }}{{T \times T_{\text{ref}} }}} \right) + \delta_{\text{A}} \times \left( {\frac{{T - T_{\text{ref}} }}{{T \times T_{\text{ref}} }}} \right)^{2} } \right]}}$$ where A ref is the net CO2-assimilation (A) at fixed reference temperature (T ref), E o(RefA) is the activation energy of A close to T ref, and δ A describes the change of E o with increasing incubation temperature (T). Similar to respiration parameters, E o(RefA) and δ A-values were strongly correlated. Symmetry of A/T curves, i.e., constancy of dE o/dT between 20–45 °C incubation temperatures, suggests close coordination of component processes underlying A. This symmetry remained at high growth temperature, despite large reductions in biochemical capacity for P i regeneration relative to carboxylation capacity (i.e., increased abundance of RubisCO activase). Acclimation to higher temperature caused pronounced reductions in physiological capacity of respiration (R Cap) (type II acclimation, determined via gas exchange measurements). Reductions in R Cap were not a result of limitations in substrate availability (i.e., pyruvate), but were related to lower abundances of mitochondrial enzymes in well-watered plants (i.e., pyruvate dehydrogenase and cytochrome oxidase). Water shortage led to sucrose accumulation, with modest reductions in mitochondrial enzyme pools. R Cap remained low when growth temperature was increased.

Contrasting response of summer soil respiration and enzyme activities to long-term warming and drought in a wet shrubland (NE Wales, UK)

Evaluating the response of soil organic matter decomposition to warming and changes in rainfall is critical to assess the likelihood of proposed positive feedbacks from the terrestrial to the atmospheric system. The response of soil respiration and extracellular activities (EEAs) to long-term warming and recurrent summer drought was studied in a wet shrubland ecosystem in Wales (UK), after 13 years of climate change simulation in a whole-ecosystem experiment. Over a year soil respiration, temperature and moisture was monitored in the field. During the summer season, coinciding with maximum soil respiration rates, soil inorganic N and P, microbial biomass and the extracellular activities (EEAs) of a selection of enzymes involved in C, N and P cycling were analysed. Based on previous field measurements of C and N mineralization, we expected a stronger response of C-cycling EEAs, in comparison to N-cycling EEAs, to drought and warming, and a greater sensitivity of C-cycling EEAs to drought than to warming. Drought had a clear impact on soil respiration during the summer season. However, the availability of inorganic N or P was not significantly affected by the treatments. Microbial biomass and C:N ratio also remained unchanged. In contrast to one of our hypothesis, C-cycling EEAs measured under non-optimal conditions that simulated soil environment in the field (pH of 4.1 and with a temperature incubation of 10°C) showed no significant differences due to long-term warming and recurring drought treatments. Possibly, this assay approach may have obscured treatment effects on the soil enzyme pool. Our results highlight the need for developing methods for the in-situ analysis of EEAs to determine rates of reactions.

Short communication: Biochemically active humic substances in contrasting agricultural managements

Because their crucial role in several soil biochemical cycles and their fast response to changes in soil management, extracellular enzymes activities are widely used as sensitive indicators of ecological change and soil quality. The aim of this work was to determine the effects of soil management on the stable pool of soil carbon cycling enzymes as indicators of essential functions. For this, extracellular β-glucosidase enzymes bounded by humic acids (C higher than 104 Da) were used to compare four long-term contrasting agricultural managements in a rainfed olive orchard representative of semi-arid Mediterranean habitats. The study was conducted for 30 years by designing a random-block of four treatments (nude vs. covered soils) and four replicates. Maintaining cover crops through fall, winter and early spring provoked a more stable and active pool of extracellular β-glucosidase in soils only if spontaneous vegetation was managed with mechanical methods. When herbicides were used during 30 years, the pattern of the molecular composition and activity of humus β-glucosidase complexes were similar in covered and nude soils, although higher activity was retrieved in the former. Tillage management increased carbon mineralization and the level of humic substances and the activity of β-glucosidase humic-bound were quite lower than in the rest of treatments. Given the ecological role of extracellular soil carbon cycling enzymes, the characterization of humus β-glucosidase complexes could be an adequate indicator of sustainability of agricultural management systems.

Effects of σ factor competition are promoter initiation kinetics dependent

In Escherichia coli, the expression of a σ factor is expected to indirectly down-regulate the expression of genes recognized by another σ factor, due to σ factor competition for a limited pool of RNA polymerase core enzymes. Evidence suggests that the sensitivity of genes to indirect down-regulation differs widely. We studied the variability in this sensitivity in promoters primarily recognized by RNAP holoenzymes carrying σ70. From qPCR and live single-cell, single-RNA measurements of the transcription kinetics of several σ70-dependent promoters in various conditions and from the analysis of σ factors population-dependent models of transcription initiation, we find that, the smaller is the time-scale of the closed complex formation relative to the open complex formation, the weaker is a promoter's responsiveness to changes in σ38 numbers. We conclude that, in E. coli, a promoter's responsiveness to indirect regulation by σ factor competition is determined by the sequence-dependent kinetics of the rate limiting steps of transcription initiation.

Heterogeneity of carbon loss and its temperature sensitivity in East-European subarctic tundra soils.

Arctic peatlands store large stocks of organic carbon which are vulnerable to the climate change but their fate is uncertain. There is increasing evidence that a part of it will be lost as a result of faster microbial mineralization. We studied the vulnerability of 3500-5900 years old bare peat uplifted from permafrost layers by cryogenic processes to the surface of an arctic peat plateau. We aimed to find biotic and abiotic drivers of CLOSS from old peat and compare them with those of adjacent, young vegetated soils of the peat plateau and mineral tundra. The soils were incubated in laboratory at three temperatures (4°C, 12°C and 20°C) and two oxygen levels (aerobic, anaerobic). CLOSS was monitored and soil parameters (organic carbon quality, nutrient availability, microbial activity, biomass and stoichiometry, and extracellular oxidative and hydrolytic enzyme pools) were determined. We found that CLOSS from the old peat was constrained by low microbial biomass representing only 0.22% of organic carbon. CLOSS was only slightly reduced by the absence of oxygen and exponentially increased with temperature, showing the same temperature sensitivity under both aerobic and anaerobic conditions. We conclude that carbon in the old bare peat is stabilized by a combination of physical, chemical and biological controls including soil compaction, organic carbon quality, low microbial biomass and the absence of plants.

Deferoxamine improves antioxidative protection in the brain of neonatal rats: The role of anoxia and body temperature

After hypoxic-ischemic insult iron deposited in the brain catalyzes formation of reactive oxygen species. Newborn rats, showing reduced physiological body temperature and their hyperthermic counterparts injected with deferoxamine (DF), a chelator of iron, are protected both against iron-mediated neurotoxicity and against depletion of low-molecular antioxidants after perinatal asphyxia. Therefore, we decided to study the effects of DF on activity of antioxidant enzymes (superoxide dismutase—SOD, glutathione peroxidase—GPx and catalase—CAT) in the brain of rats exposed neonatally to a critical anoxia at body temperatures elevated to 39°C.Perinatal anoxia under hyperthermic conditions intensified oxidative stress and depleted the pool of antioxidant enzymes. Both the depletion of antioxidants and lipid peroxidation were prevented by post-anoxic DF injection. The present paper evidenced that deferoxamine may act by recovering of SOD, GPx and CAT activity to reduce anoxia-induced oxidative stress.

Myxobacteria: Moving, Killing, Feeding, and Surviving Together.

Myxococcus xanthus, like other myxobacteria, is a social bacterium that moves and feeds cooperatively in predatory groups. On surfaces, rod-shaped vegetative cells move in search of the prey in a coordinated manner, forming dynamic multicellular groups referred to as swarms. Within the swarms, cells interact with one another and use two separate locomotion systems. Adventurous motility, which drives the movement of individual cells, is associated with the secretion of slime that forms trails at the leading edge of the swarms. It has been proposed that cellular traffic along these trails contributes to M. xanthus social behavior via stigmergic regulation. However, most of the cells travel in groups by using social motility, which is cell contact-dependent and requires a large number of individuals. Exopolysaccharides and the retraction of type IV pili at alternate poles of the cells are the engines associated with social motility. When the swarms encounter prey, the population of M. xanthus lyses and takes up nutrients from nearby cells. This cooperative and highly density-dependent feeding behavior has the advantage that the pool of hydrolytic enzymes and other secondary metabolites secreted by the entire group is shared by the community to optimize the use of the degradation products. This multicellular behavior is especially observed in the absence of nutrients. In this condition, M. xanthus swarms have the ability to organize the gliding movements of 1000s of rods, synchronizing rippling waves of oscillating cells, to form macroscopic fruiting bodies, with three subpopulations of cells showing division of labor. A small fraction of cells either develop into resistant myxospores or remain as peripheral rods, while the majority of cells die, probably to provide nutrients to allow aggregation and spore differentiation. Sporulation within multicellular fruiting bodies has the benefit of enabling survival in hostile environments, and increases germination and growth rates when cells encounter favorable conditions. Herein, we review how these social bacteria cooperate and review the main cell–cell signaling systems used for communication to maintain multicellularity.

Advances in Enzymatic Glycoside Synthesis.

A robust platform for facile defined glycan synthesis does not exist. Yet the need for such technology has never been greater as researchers seek to understand the full scope of carbohydrate function, stretching beyond the classical roles of structure and energy storage to encompass highly nuanced cell signaling events. To comprehensively explore and exploit the full diversity of carbohydrate functions, we must first be able to synthesize them in a controlled manner. Toward this goal, traditional chemical syntheses are inefficient while nature's own synthetic enzymes, the glycosyl transferases, can be challenging to express and expensive to employ on scale. Glycoside hydrolases represent a pool of glycan processing enzymes that can be either used in a transglycosylation mode or, better, engineered to function as "glycosynthases," mutant enzymes capable of assembling glycosides. Glycosynthases grant access to valuable glycans that act as functional and structural probes or indeed as inhibitors and therapeutics in their own right. The remodelling of glycosylation patterns in therapeutic proteins via glycoside hydrolases and their mutants is an exciting frontier in both basic research and industrial scale processes.

Analytic derivation of bacterial growth laws from a simple model of intracellular chemical dynamics.

Experiments have found that the growth rate and certain other macroscopic properties of bacterial cells in steady-state cultures depend upon the medium in a surprisingly simple manner; these dependencies are referred to as ‘growth laws’. Here we construct a dynamical model of interacting intracellular populations to understand some of the growth laws. The model has only three population variables: an amino acid pool, a pool of enzymes that transport an external nutrient and produce the amino acids, and ribosomes that catalyze their own and the enzymes’ production from the amino acids. We assume that the cell allocates its resources between the enzyme sector and the ribosomal sector to maximize its growth rate. We show that the empirical growth laws follow from this assumption and derive analytic expressions for the phenomenological parameters in terms of the more basic model parameters. Interestingly, the maximization of the growth rate of the cell as a whole implies that the cell allocates resources to the enzyme and ribosomal sectors in inverse proportion to their respective ‘efficiencies’. The work introduces a mathematical scheme in which the cellular growth rate can be explicitly determined and shows that two large parameters, the number of amino acid residues per enzyme and per ribosome, are useful for making approximations.