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Expression and characterization of recombinant human eosinophil-derived neurotoxin and eosinophil-derived neurotoxin-anti-transferrin receptor sFv.

The gene for the human recombinant eosinophil-derived neurotoxin (rEDN) was synthesized and fused to the gene encoding a single chain antibody (sFv) to the human transferrin receptor (EDNsFv). Both rEDN and EDNsFv were expressed as insoluble proteins in inclusion bodies in Escherichia coli BL21(DE3). Following denaturation and renaturation, EDN and EDNsFv were partially purified by chromatography on heparin-Sepharose. Final purification of EDN was achieved by Sephadex G-100, whereas EDNsFv which contained a 6-histidyl residue carboxyl terminus was highly purified using the metal chelate resin, Ni(2+)-nitriloacetic acid. Whereas the recombinant EDN had ribonuclease activity that was similar to the native protein, the fusion protein had enzymatic activity that was 6-13% that of native EDN. The fusion protein was able to bind to the human transferrin receptor. In contrast to rEDN that had no inherent cytotoxicity to human tumor cells, the EDNsFv fusion protein was cytotoxic to human leukemia cells that express the human transferrin receptor with an IC50, 0.2-1 nM. At 1.3 nM EDNsFv, no cytotoxicity was observed on cells that lack the human transferrin receptor. Free antibody to the human transferrin receptor, E6, inhibited the cytotoxicity of the EDNsFv. Human enzymes may be engineered to acquire cytotoxic properties by fusing them to antibodies. Thus, they may be candidates for the construction of immunofusion proteins that may be less immunogenic than immunotoxins containing bacterial- or plant-derived toxin moieties.

3T3 Cells↗

Isozyme-specific modules on human aldolase A molecule. Isozyme group-specific sequences 1 and 4 are required for showing characteristics as aldolase A.

Vertebrate aldolase molecules bear at least four stretches of isozyme group-specific sequences (referred to as IGS). The IGSs of the type A isozyme are known to endow the aldolase molecules with some characteristics typical of A. In order to locate the type A regions, 4 chimeric enzymes were constructed between human aldolases A and B and 5 mutant enzymes with single or double mutations in the IGS-1 region. Among engineered proteins, the chimeric enzymes bearing the type A IGS-1 to -4 (BABA34-108:306-363) and the IGS-1 and -4 (BABA34-55:306-363) exhibited similarities to isozyme A in many respects. On the other hand, neither chimeric enzyme bearing the type A IGS-1 to -3 (BAB34-108) nor that bearing the IGS-1 alone (BAB34-55) exhibited properties as isozyme A. Four mutant aldolases A (carrying single mutation in the IGS-1 region) maintained the original activity as A. Similarly, the BA306 chimera with the type B-->A substitution at positions 41 and 45 (BA306 N41K:R45S) failed to exhibit the A-like properties although the activities toward Fru-1,6-P2 and Fru-1-P significantly increased. Conclusively, the type A IGS-1, together with the IGS-4, act as indispensable modules in determining the characteristic properties of human aldolase A.

Amino Acid Sequence↗

Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide.

Random mutagenesis has been used to engineer the protease subtilisin E to function in a highly nonnatural environment--high concentrations of a polar organic solvent. Sequential rounds of mutagenesis and screening have yielded a variant (PC3) that hydrolyzes a peptide substrate 256 times more efficiently than wild-type subtilisin in 60% dimethylformamide. PC3 subtilisin E and other variants containing different combinations of amino acid substitutions are effective catalysts for transesterification and peptide synthesis in dimethylformamide and other organic media. Starting with a variant containing four effective amino acid substitutions (D60N, D97G, Q103R, and N218S; where, for example, D60N represents Asp-60-->Asn), six additional mutations (G131D, E156G, N181S, S182G, S188P, and T255A) were generated during three sequential rounds of mutagenesis and screening. The 10 substitutions are clustered on one face of the enzyme, near the active site and substrate binding pocket, and all are located in loops that connect core secondary structure elements and exhibit considerable sequence variability in subtilisins from different sources. These variable surface loops are effective handles for "tuning" the activity of subtilisin. Seven of the 10 amino acid substitutions in PC3 are found in other natural subtilisins. Great variability is exhibited among naturally occurring sequences that code for similar three-dimensional structures--it is possible to make use of this sequence flexibility to engineer enzymes to exhibit features not previously developed (or required) for function in vivo.

Amino Acid Sequence↗

Structure, mechanism and engineering of a nucleotidylyltransferase as a first step toward glycorandomization.

Metabolite glycosylation is affected by three classes of enzymes: nucleotidylyltransferases, which activate sugars as nucleotide diphospho-derivatives, intermediate sugar-modifying enzymes and glycosyltransferases, which transfer the final derivatized activated sugars to aglycon substrates. One of the first crystal structures of an enzyme responsible for the first step in this cascade, alpha-D-glucopyranosyl phosphate thymidylyltransferase (Ep) from Salmonella, in complex with product (UDP-Glc) and substrate (dTTP) is reported at 2.0 A and 2.1 A resolution, respectively. These structures, in conjunction with the kinetic characterization of Ep, clarify the catalytic mechanism of this important enzyme class. Structure-based engineering of Ep produced modified enzymes capable of utilizing 'unnatural' sugar phosphates not accepted by wild type Ep. The demonstrated ability to alter nucleotidylyltransferase specificity by design is an integral component of in vitro glycosylation systems developed for the production of diverse glycorandomized libraries.

Binding Sites↗

Engineering Pichia pastoris for biocatalysis: co-production of two active enzymes.

High levels of active glycolate oxidase from spinach (GO) and active catalase T from Saccharomyces cerevisiae (catT) have been co-produced in the methylotrophic yeast Pichia pastoris (Pp). In sequential rounds of transformation using two selectable markers, multiple copies of the genes encoding GO and catT were integrated into the Pp chromosome under control of the methanol inducible alcohol oxidase I promoter, resulting in a strain designated MSP8.6. MSP8.6 is a second-generation biocatalyst used for the conversion of glycolate to glyoxylate in the presence of a reaction component which inhibits endogenous Pp catalase. This work demonstrates a significant advance in the utility of recombinant Pp for commercial bioprocess development.

Alcohol Oxidoreductases↗

Modeling of homogeneous cloned enzyme donor immunoassay.

One of the most widely used analytical techniques for sensitive detection of biologically and clinically significant analytes is the immunoassay. In recent years direct immunoprobes allowing label-free detection of the interaction between the antibody and the target analyte have proved their capabilities as fast, simple, and nevertheless highly sensitive methods. Cloned enzyme donor immunoassay (CEDIA) homogeneous assay is based on the bacterial enzyme beta-galactosidase, which has been genetically engineered into two inactive fragments, enzyme donor and enzyme acceptor. Reassociation of the fragments in the assay forms active enzyme, which acts on substrate to generate a colored product. A comprehensive kinetic model of CEDIA is developed to aid in understanding this method and to facilitate development of a truly homogeneous version, potentially applicable to a dipstick-type multianalyte point of care analytical device (ChemChip). Although the standard assay involves a two-step process, we also chose to model a single-combined process, which would be simpler to apply in a ChemChip device. From the modeling simulation, we obtain the time courses of the amounts of product and active enzyme, from which the dynamic ranges can be obtained as 10(-6)-10(-7) and 10(-5)-10(-7)M analyte concentration for two-step and single-combined processes under the conditions of the assumed parameters, respectively. A simple one-step immunoassay has the merit of reducing time and cost and has an improved dynamic range.

Immunoenzyme Techniques↗

Homology-independent protein engineering.

Is structure, rather than sequence, the key to the successful generation of truly novel proteins? While protein evolution by homologous recombination has become an established tool to explore confined regions in sequence space, the generation of functional hybrid proteins by homology-independent methods further expands the scope of protein engineering.

Combinatorial Chemistry Techniques↗

Protein engineering of alcohol dehydrogenases: effects of amino acid changes at positions 93 and 48 of yeast ADH1.

By protein engineering we have investigated changes to two amino acid residues (Trp93 and Ser48) in the substrate pocket of yeast alcohol dehydrogenase 1. Upon changing Thr48 to serine we produced an enzyme which has markedly greater activity towards aliphatic alcohols with chain length up to 8, together with a general increase in catalytic activity (V/K). Changes at position 93 were less pronounced, with the Phe enzyme being more active than the parent towards the range of alcohols but with the alanine enzyme showing very little difference from the wild-type. Enzymes with the double changes at 48 and 93 showed increased activity towards alcohols with 3-8 carbons but the increases were not additive over the single changes. The enzymes with changes at the two positions would metabolize both stereoisomers of 2-octanol whereas the parent ADH would attack only one of them. None of the engineered enzymes would attack cyclohexanol or aromatic alcohols. The results are in general agreement with the prediction that reducing the size of amino acids in the substrate pocket would enhance the ability to oxidize alcohols larger than ethanol.

Alcohol Dehydrogenase↗

Engineering of the substrate-binding region of the subtilisin-like, cell-envelope proteinase of Lactococcus lactis.

The substrate-binding region of the cell-envelope proteinase of Lactococcus lactis strain SK11 was modelled, based on sequence homology of the catalytic domain with the serine proteinases subtilisin and thermitase. Substitutions, deletions and insertions were introduced, by site-directed and cassette mutagenesis of the prtP gene encoding this enzyme, based on sequence comparison both with subtilisin and with the homologous L.lactis strain Wg2 proteinase, which has different proteolytic properties. The engineered enzymes were investigated for thermal stability, proteolytic activity and cleavage specificity towards small chromogenic peptide substrates and the peptide alpha s1-casein(1-23). Mutations in the subtilisin-like substrate-binding region showed that Ser433 is the active site residue, and that residues 138 and 166 at either side of the binding cleft play an important role in substrate specificity, particularly when these residues and the substrate are oppositely charged. The K748T mutation in a different domain also affected specificity and stability, suggesting that this residue is in close proximity to the subtilisin-like domain and may form part of the substrate-binding site. Several mutant SK11 proteinases have novel properties not previously encountered in natural variants. Replacements of residues 137-139AKT along one side of the binding cleft produced the 137-139GPP mutant proteinase with reduced activity and narrowed specificity, and the 137-139GLA mutant with increased activity and broader specificity. Furthermore, the 137-139GDT mutant had a specificity towards alpha s1-casein(1-23) closely resembling that of L.lactis Wg2 proteinase. Mutants with an additional negative charge in the binding region were more stable towards autoproteolysis.

Amino Acid Sequence↗

Design, activity, and structure of a highly specific artificial endonuclease.

We have generated an artificial highly specific endonuclease by fusing domains of homing endonucleases I-DmoI and I-CreI and creating a new 1400 A(2) protein interface between these domains. Protein engineering was accomplished by combining computational redesign and an in vivo protein-folding screen. The resulting enzyme, E-DreI (Engineered I-DmoI/I-CreI), binds a long chimeric DNA target site with nanomolar affinity, cleaving it precisely at a rate equivalent to its natural parents. The structure of an E-DreI/DNA complex demonstrates the accuracy of the protein interface redesign algorithm and reveals how catalytic function is maintained during the creation of the new endonuclease. These results indicate that it may be possible to generate novel highly specific DNA binding proteins from homing endonucleases.

Algorithms↗

Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates.

Implementing several metabolic engineering strategies, either individually or in combination, it is possible to construct microbial plastic factories to produce a variety of polyhydroxyalkanoate (PHA) biopolymers with desirable structures and material properties. Approaches include external substrate manipulation, inhibitor addition, recombinant gene expression, host cell genome manipulation and, most recently, protein engineering of PHA biosynthetic enzymes. In addition, mathematical models and molecular methods can be used to elucidate metabolically engineered systems and to identify targets for performance improvement.

Acyltransferases↗

Engineering secondary metabolite production in plants.

Recent achievements have been made in the metabolic engineering of plant secondary metabolism. Various pathways have been altered using genes encoding biosynthetic enzymes or genes encoding regulatory proteins. In addition, antisense genes have been used to block competitive pathways, thereby increasing the flux towards the desired secondary metabolites.

Enzymes↗

Advances in enzyme technology--UK contributions.

Enzyme technology has been a recognised part of bioprocess engineering since its inception in the 1950s and 1960s. In this article the early history of enzyme technology is discussed and the subsequent developments in enzyme isolation, enzyme modification and process technology are described. These creative developments have put enzyme technology in a position of huge potential to contribute to environmentally compatible and cost effective means of industrial chemical synthesis. Recent developments in protein modification to produce designer enzymes are leading a new wave of enzyme application.

Animals↗

Use of protein engineering to explore subunit interactions in an allosteric enzyme: construction of inter-subunit hybrids in Clostridium symbiosum glutamate dehydrogenase.

Hybrids of different forms of clostridial glutamate dehydrogenase (GDH) have been constructed in order to probe the basis of allosteric interaction in this hexameric enzyme. It was shown that the C320S mutant, which is fully active and shows allosteric behaviour similar to that of the wild-type enzyme, can also be renatured after unfolding in urea. Mixtures of unfolded wild-type and C320S subunits gave rise to hybrids upon refolding. A purely random reassembly would lead to a simple binomial distribution. However there was a slightly better overall recovery of wild-type subunits and there appears to be a tendency for rapidly formed structured wild-type subunits in a mixture to nucleate further refolding in a way that biases the final distribution against the formation of C320S hexamers. Only the wild-type subunits in such hybrid mixtures are able to react with Ellman's reagent, 5,5'-dithiobis-(2-nitrobenzoate) (DTNB). Accordingly, after modification of hybrid hexamers with DTNB only the mutant subunits can bind NAD+. This permits fractionation on an NAD+-agarose affinity column. The elution pattern in itself indicates cooperativity since DTNB modification of just one subunit in a 1:5 wild-type/C320S hybrid largely abolished binding to the column. Kinetic studies were carried out on a fractionated preparation in which hexamers containing only one C320S subunit and five wild-type subunits were the predominant active species. Measurements of activity were made both before and after treatment with an excess of beta-mercaptoethanol to remove the blocking thionitrobenzoate moieties. Before beta-mercaptoethanol treatment this sample, with only one active subunit per hexamer, gave strictly hyperbolic (Michaelis-Menten) kinetics with NAD+ at pH 7.0, whereas after beta-mercaptoethanol (all six subunits now active) the markedly kinked Eadie-Hofstee plot characteristic of wild-type enzyme was obtained. On the other hand the sigmoid response to glutamate at high pH persisted (Hill coefficient=3.6) even without beta-mercaptoethanol, reflecting the fact that the inactive subunits can still bind glutamate. Beta-mercaptoethanol treatment restored full positive cooperativity (Hill coefficient=5.2). These results prove beyond doubt that the non-classical kinetic behaviour of clostridial GDH is a direct result of interaction between NAD+ binding sites on the six (normally) identical subunits of a hexamer.

Allosteric Regulation↗

Network rigidity and metabolic engineering in metabolite overproduction.

In order to enhance the yield and productivity of metabolite production, researchers have focused almost exclusively on enzyme amplification or other modifications of the product pathway. However, overproduction of many metabolites requires significant redirection of flux distributions in the primary metabolism, which may not readily occur following product deregulation because metabolic pathways have evolved to exhibit control architectures that resist flux alterations at branch points. This problem can be addressed through the use of some general concepts of metabolic rigidity, which include a means for identifying and removing rigid branch points within an experimental framework.

Carbon Dioxide↗

Genetically engineered Bifidobacterium longum for tumor-targeting enzyme-prodrug therapy of autochthonous mammary tumors in rats.

A fundamental obstacle in systemic therapy for cancer patients is the specific targeting of therapy directly to solid tumors. A strain of the domestic bacterium Bifidobacterium longum, which is non-pathogenic and anaerobic, showed selective localization to and proliferation within solid tumors after systemic application. Here, we propose a novel approach to cancer gene therapy in which anaerobic and non-pathogenic bacteria of the genus B. longum are used to achieve tumor-specific gene delivery and enzyme-prodrug therapy. We constructed a plasmid, pBLES100-S-eCD, which included eCD. Transfected B. longum produced CD in hypoxic tumors and achieved tumor site-specific conversion of 5-FC to 5-FU. Furthermore, we demonstrated antitumor efficacy in rat bearing autochthonous mammary tumors injected with the transfected B. longum directly or intravenously. This method was confirmed to be effective for enzyme-prodrug therapy not only by intratumoral injection but also by systemic administration. To estimate the toxicity of this bacterial vector, the systemic immunogenicity was evaluated by ASA reaction and the anaphylactic activity of IgG was evaluated by PCA reaction in guinea pigs. In the ASA reaction, no anaphylaxis symptoms were observed in any immunized guinea pigs injected with transfected B. longum. In the PCA reaction, B. longum/S-eCD specific-PCA-induced antibody was not detected. Thus, we proposed that anaerobic bacteria of the genus B. longum were an attractive and safe tumor-targeting vector and transfected B. longum was a potential anticancer agent that could effectively and specifically treat solid tumors.

Animals↗

Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension.

Gene splicing by overlap extension is a new approach for recombining DNA molecules at precise junctions irrespective of nucleotide sequences at the recombination site and without the use of restriction endonucleases or ligase. Fragments from the genes that are to be recombined are generated in separate polymerase chain reactions (PCRs). The primers are designed so that the ends of the products contain complementary sequences. When these PCR products are mixed, denatured, and reannealed, the strands having the matching sequences at their 3' ends overlap and act as primers for each other. Extension of this overlap by DNA polymerase produces a molecule in which the original sequences are 'spliced' together. This technique is used to construct a gene encoding a mosaic fusion protein comprised of parts of two different class-I major histocompatibility genes. This simple and widely applicable approach has significant advantages over standard recombinant DNA techniques.

Amino Acid Sequence↗

Consequences of molecular engineering enhanced DNA binding in a DNA repair enzyme.

Facilitated one-dimensional diffusion is a general mechanism utilized by several DNA-interactive proteins as they search for their target sites within large domains of nontarget DNA. T4 endonuclease V is a protein which scans DNA in a nonspecifically bound state and processively incises DNA at ultraviolet (UV)-induced pyrimidine dimer sites. An electrostatic contribution to this mechanism of target location has been established. Previous studies indicate that a decrease in the affinity of endonuclease V for nontarget DNA results in a decreased ability to scan DNA and a concomitant decrease in the ability to enhance UV survival in repair-deficient Escherichia coli. This study was designed to question the contrasting effect of an increase in the affinity of endonuclease V for nontarget DNA. With this as a goal, a gradient of increasingly basic amino acid content was created along a proposed endonuclease V-nontarget DNA interface. This incremental increase in positive charge correlated with the stepwise enhancement of nontarget DNA binding, yet inversely correlated with enhanced UV survival in repair-deficient E. coli. Further analysis suggests that the observed reduction in UV survival is consistent with the hypothesis that enhanced nontarget DNA affinity results in reduced pyrimidine dimer-specific recognition and/or binding. The net effect is a reduction in the efficiency of pyrimidine dimer incision.

Base Sequence↗