Manipulating corn germplasm to increase recombinant protein accumulation

Using plants as biofactories for industrial enzymes is a developing technology. The application of this technology to plant biomass conversion for biofuels and biobased products has potential for significantly lowering the cost of these products because of lower enzyme production costs. However, the concentration of the enzymes in plant tissue must be high to realize this goal. We describe the enhancement of the accumulation of cellulases in transgenic maize seed as a part of the process to lower the cost of these dominant enzymes for the bioconversion process. We have used breeding to move these genes into elite and high oil germplasm to enhance protein accumulation in grain. We have also explored processing of the grain to isolate the germ, which preferentially contains the enzymes, to further enhance recovery of enzyme on a dry weight basis of raw materials. The enzymes are active on microcrystalline cellulose to release glucose and cellobiose.     

Efficient,environmentally-friendly and specific valorization of lignin: promising role of non-radical lignolytic enzymes

Lignin is the second most abundant bio-resource in nature. It is increasingly important to convert lignin into high value-added chemicals to accelerate the development of the lignocellulose biorefinery. Over the past several decades, physical and chemical methods have been widely explored to degrade lignin and convert it into valuable chemicals. Unfortunately, these developments have lagged because of several difficulties, of which high energy consumption and non-specific cleavage of chemical bonds in lignin remain the greatest challenges. A large number of enzymes have been discovered for lignin degradation and these are classified as radical lignolytic enzymes and non-radical lignolytic enzymes. Radical lignolytic enzymes, including laccases, lignin peroxidases, manganese peroxidases and versatile peroxidases, are radical-based bio-catalysts, which degrade lignins through non-specific cleavage of chemical bonds but can also catalyze the radical-based re-polymerization of lignin fragments. In contrast, non-radical lignolytic enzymes selectively cleave chemical bonds in lignin and lignin model compounds and, thus, show promise for use in the preparation of high value-added chemicals. In this mini-review, recent developments on non-radical lignolytic enzymes are discussed. These include recently discovered non-radical lignolytic enzymes, their metabolic pathways for lignin conversion, their recent application in the lignin biorefinery, and the combination of bio-catalysts with physical/chemical methods for industrial development of the lignin refinery.     

适冷酶:性能与应用

由耐寒微生物产生的适冷酶显示出较高的催化活力,并常与热敏感性有关。运用X射线的结晶学理论,这一特性已开始逐渐为人所知,且控制它们对低温适应能力的机制各不相同。这些酶的应用为生物技术提供了巨大的发展潜力,例如在清洁剂和食品行业中用于生产精细化学品以及在生物环保处理中的应用。     

Rio Tinto as a niche for acidophilus enzymes of industrial relevance

Lignocellulosic residues are amongst the most abundant waste products on Earth. Therefore, there is an increasing interest in the utilization of these residues for bioethanol production and for biorefineries to produce compounds of industrial interest. Enzymes that breakdown cellulose and hemicellulose into oligomers and monosaccharides are required in these processes and cellulolytic enzymes with optimum activity at a low pH area are desirable for industrial processes. Here, we explore the fungal biodiversity of Rıo Tinto, the largest acidic ecosystem on Earth, as far as the secretion of cellulolytic enzymes is concerned. Using colorimetric and industrial substrates, we show that a high proportion of the fungi present in this extremophilic environment secrete a wide range of enzymes that are able to hydrolyze cellulose and hemicellulose at acidic pH (4.5–5). Shotgun proteomic analysis of the secretomes of some of these fungi has identified different cellulases and hemicellulolytic enzymes as well as a number of auxiliary enzymes. Supplementation of pre-industrial cocktails from Myceliophtora with Rio Tinto secretomes increased the amount of monosaccharides released from corn stover or sugar cane straw. We conclude that the Rio Tinto fungi display a good variety of hydrolytic enzymes with high industrial potential.     

High throughput screening methods for ω-transaminases

Recently, ω-transaminases have been increasingly used to synthesize amine compounds by reductive amination of prochiral ketones which are of high pharmacological significance. However, the conventional methods for evaluating these enzymes are time consuming and have often been regarded as a bottle neck in developing these enzymes as industrial biocatalysts. In the past few years, several high throughput screening methods have been developed for fast evaluation and identification of ω-transaminase. This review summarizes the various methodologies developed for rapidly screening ω-transaminases.     

Role of microbial enzymes in flavor development in foods

There are four main sources of enzymes in foods—these being the inherent enzymes, enzymes from microbial contaminants, enzymes elaborated by microorganisms added to foods, and specific enzymes added to foods. This study primarily deals with the latter two sources of enzymes in food. Although both plants and animals serve as sources of enzymes, they are not as economical or versatile sources as are enzymes obtained from microorganisms. In the meat industry, proteases are used to tenderize muscle and to obtain flavor precursors. In the preparation of cured meat products such as sausages, lipases, and proteases from bacterial cultures are utilized. Similarly, proteases and lipases are used in the dairy industry to develop flavor compounds. Proteases and amylases also have applications in the baking and milling industries where they are used to produce precursors for the nonenzymatic browning reactions. Carbohydrases such as amylase, amyloglucosidase, and glucose isomerase have found usage in the starch and syrup industry for the production of high dextrose and high fructose syrups. Other enzymes such as glucose oxidase, pectinase, and naringinase are of value to the wine and fruit juice industries. A better understanding of the mode of action of enzymes as well as the mechanisms of development of flavor compounds will further enhance the use of microbial enzymes to develop specific and desired flavors in foods.     

Mechanized techniques for the selective extraction of enzymes from plant epidermal glands

Many plant products are biosynthesized and accumulated in epidermal glands. For investigations on the metabolism of these compounds it is most convenient to obtain cell-free preparations enriched in gland contents. Two simple mechanized procedures have been developed for gently abrading the plant surface in order to efficiently extract glandular enzymes in high purity. These methods allow rapid processing of large quantities of plant material and yield extracts largely uncontaminated with materials from underlying tissue. The use of these procedures for isolating several enzymes of terpenoid metabolism is described. These techniques work especially well for microsomal enzymes and may be useful not only for enzymes found in epidermal glands but also for other enzymes localized in or near the epidermis. With simple modification, these procedures can be adapted for use with a variety of different types of plant tissues.     

PcrA/UvrD/Rep DNA helicases in bacterial genomes

Helicases, which utilize the energy liberated by the hydrolysis of nucleotides to unwind nucleic acids, are involved in many aspects of nucleic acid metabolism. Various DNA helicases from the PcrA/UvrD/Rep subfamily are essential for the survival of different pathogenic bacteria and we have recently shown that they can be inhibited with small synthetic molecules. Altogether this suggests that these enzymes are potential new drug targets. Since little is known about the presence of these enzymes in bacterial genomes, 99 bacterial genomes were analyzed in the present study. This analysis reveals which and how many of these enzymes are found in bacteria, but more important, it identifies several of these enzymes as potential drug target candidates. In addition, this work identifies several proteins, called here PURL, that have a high homology with the PcrA/UvrD/Rep proteins and that may form an additional group in this helicase subfamily.     

Glycolytic enzyme levels in synaptosomes

The specific activities of glucosephosphate isomerase, aldolase, triosephosphate isomerase, glyceraldehydephosphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase, pyruvate kinase and lactate dehydrogenase were all higher in the synaptoplasmic fraction from rat brain than in 100,000 g supernatant fraction of rat brain homogenates when the supernatants were prepared in high ionic strength solutions. Four enzymes in synaptosomes and two enzymes in homogenates were associated with particulate fractions as indicated by the large increase in specific activity of the enzymes when samples were treated with 0.3 M KCl before centrifugation. Glucosephosphate isomerase, aldolase, pyruvate kinase and lactate dehydrogenase were the enzymes that showed a large increase in specific activity following salt treatment of isolated, synaptosomal membrane while aldolase and pyruvate kinase were the two enzymes which showed a large increase in specific activity in the high speed supernatant fractions. Because the specific activities of many enzymes are found to be elevated not only in synaptosomes but in synaptosomal membrane fractions it is suggested that these enzymes may provide the potential for significantly enhanced glycolysis at these locations.     

Nature of the ferryl heme in compounds I and II

Heme enzymes are ubiquitous in biology and catalyze a vast array of biological redox processes. The formation of high valent ferryl intermediates of the heme iron (known as Compounds I and Compound II) is implicated for a number of catalytic heme enzymes, but these species are formed only transiently and thus have proved somewhat elusive. In consequence, there has been conflicting evidence as to the nature of these ferryl intermediates in a number of different heme enzymes, in particular the precise nature of the bond between the heme iron and the bound oxygen atom. In this work, we present high resolution crystal structures of both Compound I and Compound II intermediates in two different heme peroxidase enzymes, cytochrome c peroxidase and ascorbate peroxidase, allowing direct and accurate comparison of the bonding interactions in the different intermediates. A consistent picture emerges across all structures, showing lengthening of the ferryl oxygen bond (and presumed protonation) on reduction of Compound I to Compound II. These data clarify long standing inconsistencies on the nature of the ferryl heme species in these intermediates.     

Metabolite compartmentation in Saccharomyces cerevisiae.

Uninduced cultures of Saccharomyces cerevisiae exhibit high basal levels of allantoinase, allantoicase, and ureidoglycolate hydrolase, the enzymes responsible for degrading allantoin to urea. As a result, these activities increase only 4- to 8-fold upon induction, whereas the urea-degrading enzymes, urea carboxylase and allophanate hydrolase, have very low basal levels and routinely increase 30-fold on induction. Differences in the inducibility of these five enzymes were somewhat surprising because they are all part of the same pathway and have the same inducer, allophanate. Our current studies reconcile these observations. S. cerevisiae normally contained up to 1 mM allantoin sequestered in a cellular organelle, most likely the vacuole. Separation of the large amounts of allantoin and the enzymes that degrade it provide the cell with an efficient nitrogen reserve. On starvation, sequestered allantoin likely becomes accessible to these degradative enzymes. Because they are already present at high levels, the fact that their inducer is considerably removed from the input allantoin is of little consequence. This suggests that at times metabolite compartmentation may play an equal role with enzyme induction in the regulation of allantoin metabolism. Metabolism of arginine, another sequestered metabolite, must be controlled both by induction of arginase and compartmentation because arginine serves both as a reserve nitrogen source and a precursor of protein synthesis. The latter function precludes the existence of high basal levels of arginase.     

Cold-Adapted Enzymes from Marine Antarctic Microorganisms

The Antarctic marine environment is characterized by challenging conditions for the survival of native microorganisms. Indeed, next to the temperature effect represented by the Arrhenius law, the viscosity of the medium, which is also significantly enhanced by low temperatures, contributes to slow down reaction rates. This review analyses the different challenges and focuses on a key element of life at low temperatures: cold-adapted enzymes. The molecular characteristics of these enzymes are discussed as well as the adaptation strategies which can be inferred from the comparison of their properties and three-dimensional structures with those of their mesophilic counterparts. As these enzymes display a high specific activity at low and moderate temperatures associated with a relatively high thermosensitivity, the interest in these properties is discussed with regard to their current and possible applications in biotechnology.     

High pressure enhancement of enzymes: A review

While most current applications of high pressure (HP) are for inactivating deleterious enzymes, there is evidence that high pressure can induce stabilization and activation of some enzymes. Various other strategies have been employed to enhance enzyme stability, including; genetic engineering, immobilization, and operating in non-aqueous media. While each of these strategies has provided varying degrees of stability or activity enhancement, the application of high pressure may be a complementary, synergistic, or an additive enzyme enhancement technique. Over 25 enzymes that have exhibited high pressure stabilization and/or activation were compiled. Each enzyme discussed responds differently to high pressure depending on the pressure range, temperature, source, solvent or media, and substrate. Possible mechanisms for pressure-induced stabilization and activation are discussed and compared with current enzyme enhancement techniques. The compiled evidence of high pressure enzyme enhancement in this review indicates that pressure is an effective reaction parameter with potential for greater utilization in enzyme catalysis.     

Systematic and simultaneous gene profiling of 84 drug-metabolizing genes in primary human hepatocytes

Drug-metabolizing enzymes are an important battery of proteins that are involved in drug metabolism, xenobiotic detoxification, and drug-induced toxicity. Systematic, efficient, and simultaneous evaluation of drug-metabolizing gene expression in response to chemicals has a wide variety of implications in drug development, disease prevention, and personalized medicine and nutrition. In the current study, the authors have systematically and simultaneously evaluated the hepatic expression profile of drug-metabolizing enzymes in cultured human hepatocytes exposed to the xenobiotics rifampicin, omeprazole, and 3-methylcholanthrene (3-MC) using the Drug Metabolism RT(2)Profiler PCR Arrays. This new high-throughput tool allowed the authors to evaluate the expression of genes coding for 84 drug-metabolizing enzymes (including phase 1 and phase 2 drug-metabolizing enzymes and transporters) simultaneously, in a 96-well format using a small amount of experimental materials. To validate the quality of the Drug Metabolism RT(2)Profiler PCR Arrays, the PCR Array was compared with the well-documented platform TaqMan assay, and a high concordance was shown between these 2 methods, indicating the high reliability of the Drug Metabolism RT(2)Profiler PCR Arrays. In addition, increasing or decreasing the expression of drug-metabolizing enzymes by these 3 compounds was observed, and underlying mechanisms are discussed.     

Extremophilic proteases as novel and efficient tools in short peptide synthesis

The objective of this review is to outline the crucial role that peptides play in various sectors, including medicine. Different ways of producing these compounds are discussed with an emphasis on the benefits offered by industrial enzyme biotechnology. This paper describes mechanisms of peptide bond formation using a range of proteases with different active site structures. Importantly, these enzymes may be further improved chemically and/or genetically to make them better suited for their various applications and process conditions. The focus is on extremophilic proteases, whose potential does not seem to have been fully appreciated to date. The structure of these proteins is somewhat different from that of the common commercially available enzymes, making them effective at high salinity and high or low temperatures, which are often favorable to peptide synthesis. Examples of such enzymes include halophilic, thermophilic, and psychrophilic proteases; this paper also mentions some promising catalytic proteins which require further study in this respect.     

Activity patterns of phosphofructokinase,glyceraldehydephosphate dehydrogenase,lactate dehydrogenase and malate dehydrogenase in microdissected fast and slow fibres from rabbit psoas and soleus muscle

Summary Methods for standardized determination of phosphofructokinase (PFK), glyceraldehydephosphate dehydrogenase (GAPDH), lactate dehydrogenase (LDH) and malate dehydrogenase (MDH) activities in nanogram samples of microdissected single fibres of rabbit psoas and soleus muscle are described. Fast and slow fibres in soleus muscle show lower absolute activities of these enzymes than the respective fibre types in psoas muscle. Slow fibres represent a more uniform population in the two muscles according to absolute and relative activities of the enzymes investigated. Slow fibres are characterized by high activities of MDH and relatively low activities of glycolytic enzymes. Fast fibres in the soleus muscle represent a population with high activities of MDH and glycolytic enzymes. Fast fibres in psoas muscle represent a heterogeneous population with high activities of glycolytic enzymes and extremely variable activity of MDH. More than 10-fold differences exist in the MDH activities of the extreme types of this fibre population. Differences in the activity levels of MDH in single fast type fibres but also in the activities of glycolytic enzymes between fast and slow fibres are greater than those reported between extreme white and red rabbit muscles.     

Activity patterns of phosphofructokinase, glyceraldehydephosphate dehydrogenase, lactate dehydrogenase and malate dehydrogenase in microdissected fast and slow fibres from rabbit psoas and soleus muscle.

Methods for standardized determination of phosphofructokinase (PFK), glyceraldehydephosphate dehydrogenase (GAPDH), lactate dehydrogenase (LDH) and malate dehydrogenase (MDH) activities in nanogram samples of microdissected single fibres of rabbit psoas and soleus muscle are described. Fast and slow fibres in soleus muscle show lower absolute activities of these enzymes than the respective fibre types in psoas muscle. Slow fibres represent a more uniform population in the two muscles according to absolute and relative activities of the enzymes investigated. Slow fibres are characterized by high activities of MDH and relatively low activities of glycolytic enzymes. Fast fibres in the soleus muscle represent a population with high activities of MDH and glycolytic enzymes. Fast fibres in psoas muscle represent a heterogeneous population with high activities of glycolytic enzymes and extremely variable activity of MDH. More than 10-fold differences exist in the MDH activities of the extreme types of this fibre population. Differences in the activity levels of MDH in single fast type fibres but also in the activities of glycolytic enzymes between fast and slow fibres are greater than those reported between extreme white and red rabbit muscles.     

Several dehydrogenases and kinases compete for endocytosis from plasma by rat tissues.

Plasma contains many enzymes that are probably derived from damaged cells. These enzymes are cleared at characteristic rates. We showed previously that in rats the rapid clearance of alcohol dehydrogenase, lactate dehydrogenase M4 and the mitochondrial and cytosolic isoenzymes of malate dehydrogenase is largely due to endocytosis by macrophages in liver, spleen and bone marrow. We now demonstrate that uptake of each of the enzymes by these tissues is in general decreased by simultaneous injection of a high dose of one of the other dehydrogenases or a high dose of adenylate kinase or creatine kinase. A similar dose of colloidal albumin did not significantly decrease uptake of the four dehydrogenases. Nor was uptake of colloidal albumin, apo-peroxidase from horseradish or multilamellar liposomes influenced by a high dose of mitochondrial malate dehydrogenase. These results indicate that the four dehydrogenases and the two kinases are specifically endocytosed via the same receptor. We suggest that this receptor contains a group, possibly a nucleotide, with affinity for the nucleotide-binding sites of the enzymes.     

Substrate inactivation of enzymes in vitro and in vivo

Some enzymes are inactivated by their natural substrates during catalytic turnover, limiting the ultimate extent of reaction. These enzymes can be separated into three broad classes, depending on the mechanism of the inactivation process. The first type is enzymes which use molecular oxygen as a substrate. The second type is inactivated by hydrogen peroxide, which is present either as a substrate or a product, and are stabilized by high catalase activity. The oxidation of both types of enzymes shares common features with oxidation of other enzymes and proteins. The third type of enzyme is inactivated by non-oxidative processes, mainly reversible loss of cofactors or attached groups. Sub classes are defined within each broad classification based on kinetics and stoichiometry. Reaction-inactivation is in part a regulatory mechanism in vivo, because specific proteolytic systems give rapid turnover of such labelled enzymes. The methods for enhancing the stability of these enzymes under reaction conditions depends on the enzyme type. The kinetics of these inactivation reactions can be used to optimize bioreactor design and operation.