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GMAP: a multi-purpose computer program to aid synthetic gene design, cassette mutagenesis and the introduction of potential restriction sites into DNA sequences.

A computer program called GMAP has been developed for i) mapping the potential restriction endonuclease (R.E.) sites that can be introduced in a nonambiguous DNA sequence; ii) predicting the mutations required to introduce unique R.E. sites in the nonambiguous DNA sequences; and iii) searching all R.E. sites in ambiguous DNA sequence obtained by reverse translation of a given amino acid sequence. This allows the design of synthetic genes as well as the modular redesign after introducing limited base pair mismatches in wild-type genes in order to adapt them for "cassette" mutagenesis. The GMAP program uses an algorithm based on set theory that reduces the degree of complexity from an exponential to linear function of sequence length. Therefore, the speed of searching for potential R.E. sites in reverse-translated gene sequences and the prediction of new R.E. sites in natural genes by mutations are rapid.

Algorithms↗

Enzymes in diagnostics: achievements and possibilities of recombinant DNA technology.

We discuss, from an industrial point of view, the scope and possibilities of recombinant DNA technology for "diagnostic enzyme" production and application. We describe the construction of enzyme-overproducing strains and show how to simplify downstream processing, increase product quality and process profitability, improve diagnostic enzyme properties, and adjust enzymes to harsh assay conditions. We also consider some safety and environmental aspects of enzyme production. Other aspects of diagnostic enzymes that we cover are the facilitation of enzyme purification by attachment of short amino acid tails, the introduction of tails or tags for site-specific conjugation or oriented immobilization, the construction of bi- or multifunctional enzymes, and the production of enzyme-based diagnostic tests as demonstrated by the homogeneous immunoassay system of CEDIA tests. We use as examples of diagnostic enzymes glucose-6-phosphate dehydrogenase (EC 1.1.1.49), glucose oxidase (EC 1.1.3.4), alkaline phosphatase (EC 3.1.3.1), alpha-glucosidase (EC 3.2.1.20), pyruvate oxidase (EC 1.2.3.3), creatinase (EC 3.5.3.3), and beta-galactosidase (EC 3.2.1.23).

Amino Acid Sequence↗

An overview of a feasibility study for the production of industrial enzymes in transgenic alfalfa.

The overall aims of the research are to develop genetically engineered alfalfa producing high levels of industrially important enzymes and to develop rapid methods for extracting and purifying these enzymes from alfalfa juice. Using a reporter gene beta-glucuronidase (GUS) as a model system, we were able to demonstrate production of a foreign protein in alfalfa and gain valuable insight into the molecular approaches required for the expression and accumulation of foreign proteins in leaf tissue. GUS activity varied among individual transformants, and GUS was expressed in all plant tissues. GUS activity was shown to segregate in sexual progeny. There was no correlation between copy number of the GUS gene and activity. We have recently demonstrated the production of Mn-dependent lignin peroxidase and alpha-amylase in transgenic alfalfa. Concurrent research in the agricultural engineering aspects of this feasibility study focused on extraction strategies for the recovery of alfalfa juice, and on an evaluation of methods for processing and concentrating the juice. Thus, we are in a position to use plants expressing enzymes that have current or potential industrial importance to complete a feasibility study, and determine whether we can indeed economically recover target enzymes from field-grown transgenic alfalfa plants. The technology developed for these enzymes can be used to extract other value-added products from plants in the future.

Bacillus↗

Molecular mechanisms for antibody-mediated modulation of peptide-displaying enzyme sensors.

The generation of molecular sensors based on peptide-displaying enzymes for the detection of antibodies or antigens represents an innovative field of protein engineering. The knowledge of the underlying molecular mechanisms of enzymatic modulation in such sensors would be of great importance for the rational construction and improvement of responsiveness of new peptide-enzyme molecules. Here we analyze the enzymatic characteristics of three different kinds of sensors based in engineered beta-galactosidase, alkaline phosphatase and beta-lactamase, to explore a common activation basis. We describe two different categories of enzyme sensors. In one of them, including only some modified beta-lactamases, the enzymatic activity is inhibited upon ligand binding and it seems to be caused by the steric coverage of the active site by the bound antibody. In a second group, embracing members of the three studied enzymes, the ability to be modulated upon effector binding depends on the ratio between the k(cat) of the engineered enzyme and the k(cat) of the intact enzyme. This proves a common mechanism for enzymatic modulation of enzyme biosensors that is probably caused by conformational effects induced by the bound antibody on the enzyme.

Alkaline Phosphatase↗

Recent progress in biomolecular engineering.

During the next decade or so, there will be significant and impressive advances in biomolecular engineering, especially in our understanding of the biological roles of various biomolecules inside the cell. The advances in high throughput screening technology for discovery of target molecules and the accumulation of functional genomics and proteomics data at accelerating rates will enable us to design and discover novel biomolecules and proteins on a rational basis in diverse areas of pharmaceutical, agricultural, industrial, and environmental applications. As an applied molecular evolution technology, DNA shuffling will play a key role in biomolecular engineering. In contrast to the point mutation techniques, DNA shuffling exchanges large functional domains of sequences to search for the best candidate molecule, thus mimicking and accelerating the process of sexual recombination in the evolution of life. The phage-display system of combinatorial peptide libraries will be extensively exploited to design and create many novel proteins, as a result of the relative ease of screening and identifying desirable proteins. Even though this system has so far been employed mainly in screening the combinatorial antibody libraries, its application will be extended further into the science of protein-receptor or protein-ligand interactions. The bioinformatics for genome and proteome analyses will contribute substantially toward ever more accelerated advances in the pharmaceutical industry. Biomolecular engineering will no doubt become one of the most important scientific disciplines, because it will enable systematic and comprehensive analyses of gene expression patterns in both normal and diseased cells, as well as the discovery of many new high-value molecules. When the functional genomics database, EST and SAGE techniques, microarray technique, and proteome analysis by 2-dimensional gel electrophoresis or capillary electrophoresis in combination with mass spectrometer are all put to good use, biomolecular engineering research will yield new drug discoveries, improved therapies, and significantly improved or new bioprocess technology. With the advances in biomolecular engineering, the rate of finding new high-value peptides or proteins, including antibodies, vaccines, enzymes, and therapeutic peptides, will continue to accelerate. The targets for the rational design of biomolecules will be broad, diverse, and complex, but many application goals can be achieved through the expansion of knowledge based on biomolecules and their roles and functions in cells and tissues. Some engineered biomolecules, including humanized Mab's, have already entered the clinical trials for therapeutic uses. Early results of the trials and their efficacy are positive and encouraging. Among them, Herceptin, a humanized Mab for breast cancer treatment, became the first drug designed by a biomolecular engineering approach and was approved by the FDA. Soon, new therapeutic drugs and high-value biomolecules will be designed and produced by biomolecular engineering for the treatment or prevention of not-so-easily cured diseases such as cancers, genetic diseases, age-related diseases, and other metabolic diseases. Many more industrial enzymes, which will be engineered to confer desirable properties for the process improvement and manufacturing of high-value biomolecular products at a lower production cost, are also anticipated. New metabolites, including novel antibiotics that are active against resistant strains, will also be produced soon by recombinant organisms having de novo engineered biosynthetic pathway enzyme systems. The biomolecular engineering era is here, and many of benefits will be derived from this field of scientific research for years to come if we are willing to put it to good use.

Animals↗

Protein engineering of the HMG-CoA reductase of Pseudomonas mevalonii. Construction of mutant enzymes whose activity is regulated by phosphorylation and dephosphorylation.

The activity of Pseudomonas mevalonii HMG-CoA reductase (EC 1.1.1.88) is not regulated by phosphorylation, presumably due to the absence of a suitable target serine and protein kinase recognition motif. We have engineered P. mevalonii HMG-CoA reductase to a form whose activity, like that of mammalian HMG-CoA reductases, is regulated by phosphorylation/dephosphorylation. We substituted serine for arginine 387, the residue that corresponds to the regulatory serine of the HMG-CoA reductases of higher eukaryotes. A recognition motif for cAMP-dependent protein kinase was added by replacing leucine 384 by histidine (enzyme L384H/R387S) and also valine 391 by leucine (enzyme L384H/R387S/V391L). The activity of P. mevalonii HMG-CoA reductase mutant enzymes L384H/R387S and L384H/R387S/V391L was attenuated by phosphorylation. Restoration of activity accompanied subsequent dephosphorylation catalyzed by lambda protein phosphatase. Incorporation and subsequent release of phosphate paralleled the attenuation and restoration of catalytic activity. Incorporation of 0.5 mol of phosphate per subunit was accompanied by an approximately 50% decrease in initial activity. As in the analogous Syrian hamster mutant enzyme S871D, P. mevalonii mutant enzyme R387D exhibited 10% wild-type activity, suggesting that the attenuation of activity that accompanies phosphorylation results at least in part from the introduction of negative charge. Engineering of P. mevalonii HMG-CoA reductase to forms whose activity is reversibly regulated by phosphorylation/dephosphorylation provides an attractive model for future structure-based mechanistic studies. Solution of the X-ray structure of phosphorylated and dephosphorylated forms of engineered P. mevalonii HMG-CoA reductase should then reveal interactions of the active site phosphoseryl residue that result in attenuation of catalytic activity.

Animals↗

Seamless gene engineering using RNA- and DNA-overhang cloning.

Here we describe two methods for generating DNA fragments with single-stranded overhangs, like those generated by the activity of many restriction enzymes, by simple methods that do not involve DNA digestion. The methods, RNA-overhang cloning (ROC) and DNA-overhang cloning (DOC), generate polymerase chain reaction (PCR) products composed of double-stranded (ds) DNA flanked by single-stranded (ss) RNA or DNA overhangs. The overhangs can be used to recombine DNA fragments at any sequence location, creating "perfect" chimeric genes composed of DNA fragments that have been joined without the insertion, deletion, or alteration of even a single base pair. The ROC method entails using PCR primers that contain regions of RNA sequence that cannot be copied by certain thermostable DNA polymerases. Using such a chimeric primer in PCR would yield a product with a 5' overhang identical to the sequence of the RNA component of the primer, which can be used for directional ligation of the amplified product to other preselected DNA molecules. This method provides complete control over both the length and sequence of the overhangs, and eliminates the need for restriction enzymes as tools for gene engineering.

Cloning, Molecular↗

Spectral and enzymatic properties of human recombinant myeloperoxidase: comparison with the mature enzyme.

Human recombinant myeloperoxidase (recMPO), purified from an engineered Chinese hamster ovary (CHO) cell line, has been characterized and compared to the mature enzyme isolated from polymorphonuclear leukocytes. Both molecules appear essentially similar in physicochemical enzymatic terms according to the following observations. 1. The unprocessed recombinant protein displays the characteristic light absorption spectra of ferric mature MPO and exhibits its typical spectral changes in the presence of dithionite or hydrogen peroxide. 2. The addition of 14C-labeled 5-aminolevulinic acid, a heme precursor, to the culture medium of recombinant CHO cells yields labeled recMPO, indicating the presence of a heme-like structure in the molecule. 3. Like mature MPO, recMPO has a peroxidatic activity and catalyzes the oxidation of chloride ions in the presence of hydrogen peroxide, producing hypochlorous acid as measured by the monochlorodimedon assay. For both enzymes, the chlorinating activity optimally occurs around pH 5.0 at about 100 microM of hydrogen peroxide and is strongly inhibited by methimazole. 4. Diethylpyrocarbonate significantly reduces the enzymatic activity of both molecules, suggesting that histidine residues may be of prime importance in the active site of the enzymes. 5. According to infrared spectroscopy data, both enzymes present a very similar secondary structure organization. In conclusion, the data suggest that the processing of the precursor enzyme (recMPO) into the mature form occurs without major structural and functional consequences.

Animals↗

Quantitative assay system for specific enzyme activity using antibody: the case of protease, subtilisin BPN'.

Assay on a high-quality microtiter plate was found to allow for quantitative analysis of bacterial serine protease, subtilisin BPN', and its mutant enzymes which had been genetically engineered to be adapted to low-temperatures (Taguchi et al., 1998. Appl. Environ. Microbiol. 64, 492-495), by using polyclonal antibody against subtilisin BPN'. The use of polyclonal antibody was crucial in normalizing the number of various different enzyme molecules in culture supernatant samples of recombinant strains of Bacillus subtilis, giving rise to the performance of specific activity assay of the enzymes. Relative activity of each mutant subtilisin BPN' to wild-type enzyme was estimated by monitoring the increased value of absorbance caused by enzymatic hydrolysis of a chromogenic substrate. The relative activity in each enzyme estimated by this method showed good coincidence with that estimated by kinetic parameters, kcat/K(m) of the purified enzymes. We termed the system as 'ABEA' (antibody-bound enzyme assay). The efficient ABEA system developed here would be useful for the determination of specific activity of other enzymes of interest and provide us versatile applications in the field of evolutionary engineering.

Animals↗

Crystal engineering yields crystals of cyclophilin D diffracting to 1.7 A resolution.

In the pharmaceutical industry, knowledge of the three-dimensional structure of a specific target facilitates the drug-discovery process. Despite possessing favoured analytical properties such as high purity and monodispersion in light scattering, some proteins are not capable of forming crystals suitable for X-ray analysis. Cyclophilin D, an isoform of cyclophilin that is expressed in the mitochondria, was selected as a drug target for the treatment of cardiac disorders. As the wild-type enzyme defied all attempts at crystallization, protein engineering on the enzyme surface was performed. The K133I mutant gave crystals that diffracted to 1.7 A resolution using in-house X-ray facilities and were suitable for soaking experiments. The crystals were very robust and diffraction was maintained after soaking in 25% DMSO solution: excellent conditions for the rapid analysis of complex structures including crystallographic fragment screening.

Crystallization↗

Inhibition of cellulase, xylanase and beta-glucosidase activities by softwood lignin preparations.

The conversion of lignocellulosic biomass to fuel ethanol typically involves a disruptive pretreatment process followed by enzyme-catalyzed hydrolysis of the cellulose and hemicellulose components to fermentable sugars. Attempts to improve process economics include protein engineering of cellulases, xylanases and related hydrolases to improve their specific activity or stability. However, it is recognized that enzyme performance is reduced during lignocellulose hydrolysis by interaction with lignin or lignin-carbohydrate complex (LCC), so the selection or engineering of enzymes with reduced lignin interaction offers an alternative means of enzyme improvement. This study examines the inhibition of seven cellulase preparations, three xylanase preparations and a beta-glucosidase preparation by two purified, particulate lignin preparations derived from softwood using an organosolv pretreatment process followed by enzymatic hydrolysis. The two lignin preparations had similar particle sizes and surface areas but differed significantly in other physical properties and in their chemical compositions determined by a 2D correlation HSQC NMR technique and quantitative 13C NMR spectroscopy. The various cellulases differed by up to 3.5-fold in their inhibition by lignin, while the xylanases showed less variability (< or = 1.7-fold). Of all the enzymes tested, beta-glucosidase was least affected by lignin.

Cellulases↗

STADEERS: a software package for the statistical design of experiments pertaining to the estimation of parameters in rate expressions that describe enzyme-catalyzed processes.

This paper describes a computational algorithm (STADEERS--STAtistical Design of Experiments in Enzyme ReactorS) for the statistical design of biochemical engineering experiments. The type of experiment that qualifies for this package involves a batch reaction catalyzed by a soluble enzyme where the activity of the enzyme decays with time. Assuming that both the catalytic action and the deactivation of the enzyme obey known rate expressions, the present code is helpful in the process of obtaining estimates of the kinetic parameters by providing as output the times at which samples should be withdrawn from the reacting mixture. Starting D-optimal design is used as a basis for the statistical approach. This BASIC code is a powerful tool when fitting a rate expression to data because it increases the effectiveness of experimentation by helping the biochemical kineticist obtain data points with the largest possible informational content.

Algorithms↗

Protein engineering from a bioindustrial point of view.

Work with proteins, particularly enzymes, is a rapidly growing segment of the biotechnology industry. Directed evolution promises to become an increasingly important strategy in their development as it allows one to sidestep some of the difficult questions relating the structural and functional properties of such proteins to their industrial utility. It is also clear, however, that greater understanding of how to engineer certain basic enzyme properties, such as stability, activity, and surface properties, is beginning to emerge, and this understanding will make rational design more efficient. To engineer a commercially useful protein many properties need to be changed, and frequently these changes are interdependent. Recent protein engineering studies on protease, amylase, lipase and cellulase illustrate some of the progress in this area.

Journal Article↗

The effect of the layer structure on the activity of immobilized enzymes in ultrathin films.

The molecular engineering capability of the layer-by-layer (LbL) method for fabricating thin films has been exploited in order to immobilize glucose oxidase (GOD) in films with alternating layers of chitosan. Chitosan was proven a good scaffolding material, as GOD molecules preserved their catalytic activity towards glucose oxidation. Using electrochemical measurements, we showed that chitosan/GOD LbL films can be used to detect glucose with a limit of detection of 0.2 mmol l-1 and an activity of 40.5 microA mmol-1 L microg-1, which is highly sensitive when compared to other sensors in previous reports in the literature. The highest sensitivity of the LbL film was achieved when only the top layer contained GOD, thus indicating that GOD in inner layers did not contribute to glucose oxidation, probably because it hampers analyte diffusion and electron transport through the deposited layers. This may be explained by the dense packing of GOD molecules in the LbL films with chitosan, as inferred from estimates of the amount of GOD adsorbed per layer using a quartz crystal microbalance.

Aspergillus niger↗

Progress in monoamine oxidase (MAO) research in relation to genetic engineering.

Monoamine oxidase (MAO) is an enzyme that oxidizes various physiologically and pathologically important monoamine neurotransmitters and hormones such as dopamine, noradrenaline, adrenaline, and serotonin. Two types of MAO, i.e. type A (MAO-A) and type B (MAO-B), were first discovered pharmacologically. MAO-A is inhibited by clorgyline; and MAO-B, by deprenyl. cDNAs MAO-A and MAO-B were cloned and their structures determined. MAO-A and MAO-B are made of similar but different polypeptides and encoded by different nuclear genes located on the X chromosome (Xp11.23). MAO-A and MAO-B genes consist of 15 exons with identical intron-exon organization, suggesting that they were derived from a common ancestral gene. Both enzymes require a flavin cofactor, flavin adenine dinucleotide (FAD), which binds to the cysteine residue of a pentapeptide sequence (Ser-Gly-Gly-Cys-Tyr). Both enzymes exist on the outer membrane of mitochondria of various types of cells in various tissues including the brain. In humans, MAO-A is abundant in the brain and liver, whereas the liver, lungs and intestine are rich in MAO-B. MAO-A oxidizes noradrenaline and serotonin; and MAO-B, mainly beta-phenylethylamine. In the human brain, MAO-A exists in catecholaminergic neurons, but MAO-B is found in serotonergic neurons and glial cells. MAO-A knockout mice exhibit increased serotonin levels and aggressive behavior, whereas MAO-B knockout mice show little behavioral change. The gene knockout mice of MAO-A or MAO-B, together with the observation that some humans lack MAO-A, MAO-B, or both have contributed to our understanding of the function of MAO-A and MAO-B in health and disease. MAO-A and MAO-B may be closely related to various neuropsychiatric disorders such as depression and Parkinson's disease, and inhibitors of them are the subject of drug development for such diseases.

Animals↗

Development of a bisphenol A-adsorbing yeast by surface display of the Kluyveromyces yellow enzyme on Pichia pastoris.

A novel surface-engineered strain of yeast Pichia pastoris was constructed that displays at its surface Kluyveromyces lactis Yellow Enzyme (KYE) fused to the C-terminal half of Saccharomyces cerevisiae alpha-agglutinin. The expression of the fusion protein was controlled by the AOX1-promoter. The new strain showed an increased sorption of the xenoestrogen Bisphenol A (BPA). It was shown that sorption of BPA depended on the presence of methanol in the growth medium and on the pH of the binding assays. The binding kinetics were typical for binding at a surface. The present results demonstrate that the alpha-agglutinin surface display system can be used in the yeast P. pastoris.

Adsorption↗

[Molecular biology and gene engineering of phytase].

Phytase is a new-style enzyme used in monogastric animal feed. The addition of phytase to feed can increase phosphorus availability, decrease environmental phosphorus pollution and improve the performance of animal. This paper reviews the research progress and trend in recent studies related to molecular biology and gene engineering of phytase.

6-Phytase↗