Metagenomics approach to identify lignocellulose-degrading enzymes in the gut microbiota of the Chinese bamboo rat cecum

BACKGROUND: Lignocellulose is considered a renewable organic material, but the industrial production of biofuel from lignocellulose is challenging because of the lack of highly active hydrolytic enzymes. The guts of herbivores contain many symbiotic microorganisms that have evolved to hydrolyze plant lignocellulose. Chinese bamboo rats mainly consume high-fiber foods, indicating that some members of the intestinal tract microbiota digest lignocellulose, providing these rats with the energy required for growth. RESULTS: Here, we used metagenomics to analyze the diversity and functions of the gut microbiota in Chinese bamboo rats. We identified abundant populations of lignocellulose-degrading bacteria, whose main functions involved carbohydrate, amino acid, and nucleic acid metabolism. We also found 587 carbohydrate-active enzyme genes belonging to different families, including 7 carbohydrate esterase families and 21 glycoside hydrolase families. The glycoside hydrolase 3, glycoside hydrolase 1, glycoside hydrolase 43, carbohydrate esterase 4, carbohydrate esterase 1, and carbohydrate esterase 3 families demonstrated outstanding performance. CONCLUSIONS: The microbes and enzymes identified in our study expand the existing arsenal of proficient degraders and enzymes for lignocellulosic biofuel production. This study also describes a powerful approach for targeting gut microbes and enzymes in numerous industries.

Advances of enzymes in the applications of disease treatment and drug preparation / 生物工程学报

The development of biotechnology and the in-depth research on disease mechanisms have led to increased application of enzymes in the treatment of diseases. In addition, enzymes have shown great potential in drug manufacturing, particularly in production of non-natural organic compounds, due to the advantages of mild reaction conditions, high catalytic efficiency, high specificity, high selectivity and few side reactions. Moreover, the application of genetic engineering, chemical modification of enzymes and immobilization technologies have further improved the function of enzymes. This review summarized the advances of using enzymes as drugs for disease treatment or as catalysts for drug manufacturing, followed by discussing challenges, potential solutions and future perspectives on the application of enzymes in the medical and pharmaceutical field.

Impact of metabolic enzymes overexpression on transient expression of anti-hLAG3 by CHO cells / 生物工程学报

To enhance recombinant protein production by CHO cells, We compared the impact of overexpression of metabolic enzymes, namely pyruvate carboxylase 2 (PYC2), malate dehydrogenase Ⅱ (MDH2), alanine aminotransferase Ⅰ (ALT1), ornithine transcarbamylase (OTC), carbamoyl phosphate synthetase Ⅰ (CPSⅠ), and metabolism related proteins, namely taurine transporter (TAUT) and Vitreoscilla hemoglobin (VHb), on transient expression of anti-hLAG3 by ExpiCHO-S. Overexpression of these 7 proteins could differentially enhance antibody production. OTC, CPSI, MDH2, and PYC2 overexpression could improve antibody titer by 29.2%, 27.6%, 24.1%, and 20.3%, respectively. Specifically, OTC and MDH2 could obviously improve early-stage antibody production rate and the culture period was shortened by 4 days compared with that of the control. In addition, OTC and MDH2 had little impact on the affinity of anti-hLAG3. In most cases, overexpression of these proteins had little impact on the cell growth of ExpiCHO-S. MDH2 and ALT1 overexpression in H293T cells could also improve antibody production. Overall, overexpression of enzymes involved in cellular metabolism is an effective tool to improve antibody production in transient expression system.

Research progress of Pictet-Spenglerases / 生物工程学报

Pictet-Spenglerases (P-Sases) catalyze the Pictet-Spengler (P-S) reactions and exhibit high stereoselectivity and regioselectivity under mild conditions. The typical P-S reaction refers to the condensation and recyclization of β-arylethylamine with aldehyde or ketone under acidic conditions to form tetrahydroisoquinoline and β-carboline alkaloid derivatives. The related enzymatic products of P-Sases are the backbones of various bioactive compounds, including clinical drugs: morphine, noscapine, quinine, berberine, ajmaline, morphine. Furthermore, the activity of P-Sases in stereoselective and regioselective catalysis is also valuable for chemoenzymatic synthesis. Therefore, this review summarizes the research progress in the discovery, functional identification, biological characteristics and catalytic applications of P-Sases, which provide the useful theoretical reference in future P-Sases research and development.

Assessment of wasteland derived biomass for bioethanol production

Background: The bioethanol produced from biomass is a promising alternative fuel. The lignocellulose from marginal areas or wasteland could be a promising raw material for bioethanol production because it is present in large quantities, is cheap, renewable and has favorable environmental properties. Despite these advantages, lignocellulosic biomass is much more difficult to process than cereal grains, due to the need for intensive pretreatment and relatively large amounts of cellulases for efficient hydrolysis. Therefore, there is a need to develop an efficient and cost-effective method for the degradation and fermentation of lignocellulosic biomass to ethanol. Results: The usefulness of lignocellulosic biomass from wasteland for the production of bioethanol using pretreatment with the aid of ionic liquids of 1-ethyl-3-methylimidazolium acetate and 1-ethyl-3-methylimidazolium chloride was evaluated in this study. The pretreatment process, enzymatic hydrolysis and alcoholic fermentation lasted a total of 10 d. The largest amounts of bioethanol were obtained from biomass originating from agricultural wasteland, in which the dominant plant was fireweed (Chamaenerion angustifolium) and from the field where the common broom (Cytisus scoparius) was the dominant. Conclusions: The plants such as fireweed, common broom, hay and goldenrod may be useful for the production of liquid biofuels and it would be necessary in the further stage of research to establish and optimize the conditions for the technology of ethyl alcohol producing from these plant species. Enzymatic hydrolysis of biomass from agricultural wastelands results in a large increase in fermentable sugars, comparable to the enzymatic hydrolysis of rye, wheat, rice or maize straw.

Development of biodegradation process for Poly(DL-lactic acid) degradation by crude enzyme produced by Actinomadura keratinilytica strain T16-1

Background: Plastic waste is a serious problem because it is difficult to degrade, thereby leading to global environment problems. Poly(lactic acid) (PLA) is a biodegradable aliphatic polyester derived from renewable resources, and it can be degraded by various enzymes produced by microorganisms. This study focused on the scale-up and evaluated the bioprocess of PLA degradation by a crude microbial enzyme produced by Actinomadura keratinilytica strain T16-1 in a 5 L stirred tank bioreactor. Results: PLA degradation after 72 h in a 5 L bioreactor by using the enzyme of the strain T16-1 under controlled pH conditions resulted in lactic acid titers (mg/L) of 16,651 mg/L and a conversion efficiency of 89% at a controlled pH of 8.0. However, the PLA degradation process inadvertently produced lactic acid as a potential inhibitor, as shown in our experiments at various concentrations of lactic acid. Therefore, the dialysis method was performed to reduce the concentration of lactic acid. The experiment with a dialysis bag achieved PLA degradation by weight loss of 99.93%, whereas the one without dialysis achieved a degradation of less than approximately 14.75%. Therefore, the dialysis method was applied to degrade a commercial PLA material (tray) with a conversion efficiency of 32%, which was 6-fold more than that without dialysis. Conclusions: This is the first report demonstrating the scale-up of PLA degradation in a 5 L bioreactor and evaluating a potential method for enhancing PLA degradation efficiency.

Modeling of lactose enzymatic hydrolysis using Monte Carlo method

Background: Mathematical modeling is useful in the analysis, prediction, and optimization of an enzymatic process. Unlike the conventional modeling methods, Monte Carlo method has special advantages in providing representations of the molecule's spatial distribution. However, thus far, Monte Carlo modeling of enzymatic system is namely based on unimolecular basis, not suitable for practical applications. In this research, Monte Carlo modeling is performed for enzymatic hydrolysis of lactose for the purpose of real-time applications. Results: The enzyme hydrolysis of lactose, which is conformed to Michaelis­Menten kinetics, is modeled using the Monte Carlo modeling method, and the simulation results prove that the model predicts the reaction kinetics very well. Conclusions: Monte Carlo modeling method can be used to model enzymatic reactions in a simple way for real-time applications.

Hydrolytic efficiency and isomerization during de-esterification of natural astaxanthin esters by saponification and enzymolysis

Background: Astaxanthin from natural sources is typically esterified with fatty acids; hence, it must be hydrolyzed to remove esters before identification and quantification by conventional HPLC. Alkaline-catalyzed saponification and enzyme-catalyzed enzymolysis are the most commonly used de-esterification methods. However, information on the efficiency and isomerization during de-esterification of natural astaxanthin esters by these two methods remains scarce. Therefore, we conducted two HPLC-based experiments to determine which method is better for hydrolyzing astaxanthin esters. Results: To assess the effect of enzymolysis (0.67 U/mL cholesterol esterase, at 37°C) and saponification (0.021 M NaOH, at 5°C) conditions on free astaxanthin recovery and destruction or structural transformation of astaxanthin, we varied the total treatment time across a range of 195 min. The results showed that enzymolysis and saponification were complete in 60 min and 90 min, respectively. After complete hydrolysis, the maximum free astaxanthin recovery obtained by enzymolysis was 42.6% more than that obtained by saponification. The identification of by-products, semi-astacene and astacene, during the process of saponification also indicated that a more severe degradation of astaxanthin occurred during saponification. Moreover, the composition of astaxanthin isomers during saponification was similar to that of the isomers during enzymolysis between 30 min and 75 min (all-trans:9-cis:13-cis = 21:3:1, approximately) but dramatically changed after 90 min, whereas the composition in the enzymolysis treatment remained relatively stable throughout. Conclusion: Compared with saponification, enzymolysis with cholesterol esterase was recommended as a more accurate method for de-esterification of natural astaxanthin esters for further qualitative and quantitative HPLC analysis.

Enzymatic reactions involving the heteroatoms from organic substrates

ABSTRACT Several enzymatic reactions of heteroatom-containing compounds have been explored as unnatural substrates. Considerable advances related to the search for efficient enzymatic systems able to support a broader substrate scope with high catalytic performance are described in the literature. These reports include mainly native and mutated enzymes and whole cells biocatalysis. Herein, we describe the historical background along with the progress of biocatalyzed reactions involving the heteroatom(S, Se, B, P and Si) from hetero-organic substrates.

Poly(DL-lactide)-degrading enzyme production by immobilized Actinomadura keratinilytica strain T16-1 in a 5-L fermenter under various fermentation processes

Background: Poly(DL-lactic acid), or PDLLA, is a biodegradable polymer that can be hydrolyzed by various types of enzymes. The protease produced by Actinomadura keratinilytica strain T16-1 was previously reported to have PDLLA depolymerase activity. However, few studies have reported on PDLLA-degrading enzyme production by bacteria. Therefore, the aims of this study were to determine a suitable immobilization material for PDLLA-degrading enzyme production and optimize PDLLA-degrading enzyme production by using immobilized A. keratinilytica strain T16-1 under various fermentation process conditions in a stirrer fermenter. Results: Among the tested immobilization materials, a scrub pad was the best immobilizer, giving an enzyme activity of 30.03 U/mL in a shake-flask scale. The maximum enzyme activity was obtained at aeration 0.25 vvm, agitation 170 rpm, 45°C, and 48 h of cultivation time. Under these conditions, a PDLLA-degrading enzyme production of 766.33 U/mL with 15.97 U/mL·h productivity was observed using batch fermentation in a 5-L stirrer fermenter. Increased enzyme activity and productivity were observed in repeated-batch (942.67 U/mL and 19.64 U/mL·h) and continuous fermentation (796.43 U/mL and 16.58 U/mL·h) at a dilution rate of 0.013/h. Scaled-up production of the enzyme in a 10-L stirrer bioreactor using the optimized conditions showed a maximum enzyme activity of 578.67 U/mL and a productivity of 12.06 U/mL·h. Conclusions: This research successfully scaled-up the enzyme production to 5 and 10 L in a stirrer fermenter and is helpful for many applications of poly(lactic acid).

Induction of defense-related enzymes in patchouli inoculated with virulent Ralstonia solanacearum

Background: Defense-related anti-oxidative response is a vital defense mechanism of plants against pathogen invasion. Ralstonia solanacearum is an important phytopathogen. Bacterial wilt caused by R. solanacearum is the most destructive disease and causes severe losses in patchouli, an important aromatic and medicinal plant in Southeast Asia. The present study evaluated the defense response of patchouli inoculated with virulent R. solanacearum. Results: Results showed that the basic enzymatic activities differed not only between the leaves and stems but also between the upper and lower parts of the same organ of patchouli. POD, SOD, PPO, and PAL enzymatic activities were significantly elevated in leaves and stems from patchouli inoculated with R. solanacearum compared to those in control. The variation magnitude and rate of POD, PPO, and PAL activities were more obvious than those of SOD in patchouli inoculated with R. solanacearum. PAGE isoenzymatic analysis showed that there were one new POD band and two new SOD bands elicited, and at least two isoformic POD bands and two SOD bands were observably intensified compared to the corresponding control. Conclusion: Our results suggest that not only defense-related enzymatic activities were elevated but also the new isoenzymatic isoforms were induced in patchouli inoculated with R. solanacearum.

Highly efficient enzymatic preparation of isomalto-oligosaccharides from starch using an enzyme cocktail

Background: Current commercial production of isomalto-oligosaccharides (IMOs) commonly involves a lengthy multistage process with low yields. Results: To improve the process efficiency for production of IMOs, we developed a simple and efficient method by using enzyme cocktails composed of the recombinant Bacillus naganoensis pullulanase produced by Bacillus licheniformis, α-amylase from Bacillus amyloliquefaciens, barley bran ß-amylase, and α-transglucosidase from Aspergillus niger to perform simultaneous saccharification and transglycosylation to process the liquefied starch. After 13 h of reacting time, 49.09% IMOs (calculated from the total amount of isomaltose, isomaltotriose, and panose) were produced. Conclusions: Our method of using an enzyme cocktail for the efficient production of IMOs offers an attractive alternative to the process presently in use.

NaCl stress impact on the key enzymes in glycolysis from Lactobacillus bulgaricus during freeze-drying

Abstract The viability of Lactobacillus bulgaricus in freeze-drying is of significant commercial interest to dairy industries. In the study, L.bulgaricus demonstrated a significantly improved (p < 0.05) survival rate during freeze-drying when subjected to a pre-stressed period under the conditions of 2% (w/v) NaCl for 2 h in the late growth phase. The main energy source for the life activity of lactic acid bacteria is related to the glycolytic pathway. To investigate the phenomenon of this stress-related viability improvement in L. bulgaricus, the activities and corresponding genes of key enzymes in glycolysis during 2% NaCl stress were studied. NaCl stress significantly enhanced (p < 0.05) glucose utilization. The activities of glycolytic enzymes (phosphofructokinase, pyruvate kinase, and lactate dehydrogenase) decreased during freeze-drying, and NaCl stress were found to improve activities of these enzymes before and after freeze-drying. However, a transcriptional analysis of the corresponding genes suggested that the effect of NaCl stress on the expression of the pfk2 gene was not obvious. The increased survival of freeze-dried cells of L. bulgaricus under NaCl stress might be due to changes in only the activity or translation level of these enzymes in different environmental conditions but have no relation to their mRNA transcription level.

Impact of pectolytic enzyme on the fermentation time and free-run juice rate of Sharad red wine.

We evaluated the effect of addition of commercially available pectolytic enzyme preparations in the must from Sharad variety, cultivated in India and its influence on some oenological parameters of red wine. The small scale fermentations demonstrated marked difference of organoleptic (colour) and rheologic characteristics (filterability, settling rates) and aroma between enzyme treated samples and control samples. We observed 29% enhancement in free-run juice yield and a remarkable 43% reduction in the fermentation time compared to the control. This biotechnological approach has demonstrated the economic feasibility and the benefits of adding 0.05 g. Kg-1 grapes pectolytic enzyme in terms of yield, aroma, colour, clarity and fermentation period.

Modulation of small intestinal homeostasis along with its microflora during acclimatization at simulated hypobaric hypoxia.

At high altitude (HA) hypobaric hypoxic environment manifested several pathophysiological consequences of which gastrointestinal (GI) disorder are very common phenomena. To explore the most possible clue behind this disorder intestinal flora, the major player of the GI functions, were subjected following simulated hypobaric hypoxic treatment in model animal. For this, male albino rats were exposed to 55 kPa (~ 4872.9 m) air pressure consecutively for 30 days for 8 h/day and its small intestinal microflora, their secreted digestive enzymes and stress induced marker protein were investigated of the luminal epithelia. It was observed that population density of total aerobes significantly decreased, but the quantity of total anaerobes and Escherichia coli increased significantly after 30 days of hypoxic stress. The population density of strict anaerobes like Bifidobacterium sp., Bacteroides sp. and Lactobacillus sp. and obligate anaerobes like Clostridium perfringens and Peptostreptococcus sp. were expanded along with their positive growth direction index (GDI). In relation to the huge multiplication of anaerobes the amount of gas formation as well as content of IgA and IgG increased in duration dependent manner. The activity of some luminal enzymes from microbial origin like α-amylase, gluco-amylase, proteinase, alkaline phosphatase and β-glucuronidase were also elevated in hypoxic condition. Besides, hypoxia induced in formation of malondialdehyde along with significant attenuation of catalase, glutathione peroxidase, superoxide dismutase activity and lowered GSH/GSSG pool in the intestinal epithelia. Histological study revealed disruption of intestinal epithelial barrier with higher infiltration of lymphocytes in lamina propia and atrophic structure. It can be concluded that hypoxia at HA modified GI microbial imprint and subsequently causes epithelial barrier dysfunction which may relate to the small intestinal dysfunction at HA.

Kinetic modelling of coupled transport across biological membranes.

In this report, we have modelled a secondary active co-transporter (symport and antiport), based on the classical kinetics model. Michaelis-Menten model of enzyme kinetics for a single substrate, single intermediate enzyme catalyzed reaction was proposed more than a hundred years ago. However, no single model for the kinetics of co-transport of molecules across a membrane is available in the literature. We have made several simplifying assumptions and have followed the basic Michaelis-Menten approach. The results have been simulated using GNU Octave. The results will be useful in general kinetic simulations and modelling.

Enzymatic modulation as a basis of therapeutics.

Enzyme inhibition has emerged as an important area in development of therapeutics. The basis of a large number of therapeutics used in modern day medicine for treatment of various aliments is enzyme inhibition. This review is a compilation of nearly all the therapeutic entities, currently in use, embracing almost each area of therapy including antibacterial, antifungal, antiviral, antimalarials, anticancer, antihypertensive, diuretics, antianginals, antithromboembolics, hypolipidemics, cardiotonics, anti-inflammatory, analgesics, antipyretics, antigout, antiasthamatics, antidepressants, cognition enhancers, antidiabetics, antithyroid drugs, drugs used for myasthenia gravis, peptic ulcer, parkinson’s disease, BHP, osteoarthritis, glaucoma, erectile dysfunction, septic shock, inflammation and/or neuro-degenerative disorders.

Relationship between PMI and relative expression of myocardial various RNAs in rats died of different causes / 法医学杂志

OBJECTIVE@#To observe the changes of relative expression of myocardial various RNAs in rats died of different causes and their relationship with PMI.@*METHODS@#The rat models were established in which the rats were sacrificed by broken neck, asphyxia, and hemorrhagic shock. Total RNAs were extracted from myocardium. The quantitative real time PCR was used to calculate threshold cycle values of RNAs including glyceraldehyde-3-phosphate dehydrogenase (GAPDH), beta-actin, inducible nitric oxide synthase (iNOS), hypoxia-inducible factor-1 (HIF-1), tumor necrosis factor-alpha (TNF-alpha), interleukin-6 (IL-6), and U6 small nuclear RNA (U6 snRNA) and to study the changes of the relative expressions of various indexes with PMI.@*RESULTS@#U6 snRNA with stable expression level could be used as appropriate internal control. In the early PMI, the relative expression of GAPDH, HIF-1, iNOS, TNF-alpha, and IL-6 more characteristically increased in groups of asphyxia and hemorrhagic shock than in group of broken neck, but the quantity of beta-actin decreased in all groups. In the late PMI, all the relative expressions significantly declined in correlation with the degradation of RNA.@*CONCLUSION@#The characteristic changes of each RNA expression can be used as references to estimate PMI in deaths by different causes.

Optimization of enzymatic saccharification of microwave pretreated sugarcane tops through response surface methodology for biofuel.

The optimization of biomass loading enzyme loading, surfactant concentration and incubation time, using response surface methodology (RSM) and Box Behnken design for enzymatic saccharification of sugarcane tops (SCT) for maximum recovery of fermentable sugars using crude cellulases, resulted in 90.24% saccharification efficiency. Maximum saccharification yield of 0.376 g/g glucose as substrate for ethanol production was observed at optimal conditions of 10% biomass loading (pretreated), 100FPU/g of cellulase loading, 0.04% (w/w) surfactant concentration and 72 h of incubation time.

A roadmap to directed enzyme evolution and screening systems for biotechnological applications

Enzymes have been long used in man-made biochemical processes, from brewing and fermentation to current industrial production of fine chemicals. The ever-growing demand for enzymes in increasingly specific applications requires tailoring naturally occurring enzymes to the non-natural conditions found in industrial processes. Relationships between enzyme sequence, structure and activity are far from understood, thus hindering the capacity to design tailored biocatalysts. In the field of protein engineering, directed enzyme evolution is a powerful algorithm to generate and identify novel and improved enzymes through iterative rounds of mutagenesis and screening applying a specific evolutive pressure. In practice, critical checkpoints in directed evolution are: selection of the starting point, generation of the mutant library, development of the screening assay and analysis of the output of the screening campaign. Each step in directed evolution can be performed using conceptually and technically different approaches, all having inherent advantages and challenges. In this article, we present and discuss in a general overview, challenges of designing and performing a directed enzyme evolution campaign, current advances in methods, as well as highlighting some examples of its applications in industrially relevant enzymes.