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PubMed1985

Chemical modifications and genetic engineering of food proteins.

Relationships of structure to function of proteins can be studied using chemical modifications of amino-acid side chains and, more recently, recombinant deoxyribonucleic acid techniques to alter primary sequences. A wide array of chemical modifications are available to the food chemist for manipulating the functionality of food proteins. The esterification of side-chain carboxyl groups in proteins to yield polycationic polymers is emphasized in this review as an example of changing the functionality of a protein via chemical derivatization. However, chemical modifications of proteins generally suffer from a lack of control in the extent of derivatization attainable, oftentimes yielding polydisperse products. Recent advances in recombinant deoxyribonucleic acid technology offer the opportunity to relate systematically well-defined alterations in the primary sequence to changes in protein functionality. Using oligonucleotide-directed mutagenesis, one can now use synthetic oligodeoxynucleotides to prepare semisynthetic genes coding for specific changes in the primary sequence of proteins. Incorporation of the altered genes into an appropriate host can lead to the production of the modified protein for structure-function relationship studies. These recombinant deoxyribonucleic acid techniques may eventually provide the means to engineer proteins and enzymes.

Circular Dichroism↗
PubMed1991

Engineering of functional supramacromolecular complexes of proteins (enzymes) using reversed micelles as matrix microreactors.

The size of the inner water cavity of reversed micelles formed in a triple system 'water-surfactant-organic solvent' can be widely varied by changing the degree of surfactant hydration. This gives grounds to use reversed micelles as matrix microreactors for the design of supramolecular complexes of proteins. Using ultracentrifugation analysis, it has been demonstrated that the oligomeric composition of various enzymes (ketoglutarate dehydrogenase, alkaline phosphatase, lactic dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase) solubilized in reversed micelles of Aerosol OT [sodium bis(2-ethylehexyl)sulfosuccinate] in octane changes upon variation of the degree of hydration. An oligomeric complex forms under conditions when the radius of the micelle inner cavity is big enough to incorporate this complex as a whole. At lower degrees of hydration the micelles 'uncouple' such complexes to their components. The catalytic properties of various oligomeric complexes have been studied. Possibilities of using reversed micelles for the separation of subunits of oligomeric enzymes under non-denaturating conditions have been demonstrated. In particular, the isolated subunits of alkaline phosphatase, lactic dehydrogenase and glyceraldehyde-3-phosphate have been found to be active in Aerosol OT reversed micelles. The dependences of the catalytic activity of oligomeric enzymes represent saw-like curves. The maxima of the catalytic activity observed at these curves relate to the functioning of various oligomeric forms of an enzyme. The radii of the micelle inner cavity under conditions when these maxima are observed correlate with the linear dimensions of the enzyme oligomeric forms. Correlation of the position of a maximum with the shape of an oligomeric complex is discussed.

Alkaline Phosphatase↗
PubMed2005

Novel protein purification system utilizing an N-terminal fusion protein and a caspase-3 cleavable linker.

Coupled with over-expression in host organisms, fusion protein systems afford economical methods to obtain large quantities of target proteins in a fast and efficient manner. Some proteases used for these purposes cleave C-terminal to their recognition sequences and do not leave extra amino acids on the target. However, they are often inefficient and are frequently promiscuous, resulting in non-specific cleavages of the target protein. To address these issues, we created a fusion protein system that utilizes a highly efficient enzyme and leaves no residual amino acids on the target protein after removal of the affinity tag. We designed a glutathione S-transferase (GST)-fusion protein vector with a caspase-3 consensus cleavage sequence located between the N-terminal GST tag and a target protein. We show that the enzyme efficiently cleaves the fusion protein without leaving excess amino acids on the target protein. In addition, we used an engineered caspase-3 enzyme that is highly stable, has increased activity relative to the wild-type enzyme, and contains a poly-histidine tag that allows for efficient removal of the enzyme after cleavage of the fusion protein. Although we have developed this system using a GST tag, the system is amenable to any commercially available affinity tag.

Amino Acid Sequence↗
PubMed2026

Cre-loaded integrase-defective lentiviral vectors for targeted cassette exchange in CHO cells.

Genome-modifying enzymes, such as recombinases and CRISPR-associated nucleases, enable targeted gene insertion when delivered transiently to minimize off-target effects. Precise genome engineering requires controlled enzyme activity, as well as efficient donor DNA transfer. Integrase-defective lentiviral vectors (IDLVs) provide a promising platform for transient episomal DNA transfer; however, their integration efficiency depends on complementary genome-targeting strategies. Here, we engineered Cre-loaded IDLVs (Cre-IDLVs) that co-package lentiviral vector genomes together with bioactive Cre recombinase. Cre was inserted into the Gag region of an integrase-defective gag-pol construct, allowing for efficient encapsidation and protease-mediated release during virion maturation without compromising the viral titer. The resulting particles carried donor cassettes flanked by heterospecific loxP sites. When applied to CHO founder cells harboring compatible genomic loxP landing pads, Cre-IDLVs efficiently mediated recombination-mediated cassette exchange, producing the highest number of G418-resistant colonies among the plasmid ratios tested. Genomic PCR and sequencing confirmed precise locus-specific insertion without detectable random integration in the analyzed clones. These findings establish Cre-IDLVs as a streamlined dual-delivery platform that couples transient recombinase activity with episomal donor DNA transfer. This hybrid lentiviral strategy provides a programmable approach for controlled and site-specific genome modification in mammalian cells.

Integrases↗
PubMed2025

A Sequence Motif Enables Widespread Use of Non-Canonical Redox Cofactors in Natural Enzymes.

Non-canonical redox cofactors (NRCs) are promising alternatives to nicotinamide adenine dinucleotide (phosphate) (NAD(P)+) for biomanufacturing due to low cost and exquisite electron delivery control, yet their adoption is limited by the scarcity of compatible enzymes. Here, we screened the aldehyde dehydrogenase (ALDH) protein family and identified a conserved RH/QxxR sequence motif that enables widespread NRC activity among natural enzymes. Bos taurus ALDH3a1 and Pseudanabaena biceps ALDH exhibit unprecedented turnover with nicotinamide mononucleotide (NMN+), with kcat values matching or exceeding that of NAD+ and surpassing most engineered NRC-active enzymes by 10 to 105-fold, based on the relative NRC to native activity. Structural and dynamic analyses reveal this motif reinforces cofactor positioning and pre-organizes the active site without dependence on the adenosine monophosphate moiety of NAD+. When introduced into diverse ALDH scaffolds, the RH/QxxR motif enhances NMN+ activity up to 60-fold. In addition to NMN+, this motif also supports activity across multiple non-nucleotide, simple synthetic NRCs such as 1-(2-carbamoylmethyl)nicotinamide (AmNA+). These findings elucidate Nature's solution to the engineering challenge of obtaining NRC-active enzymes and offers a blueprint to mine latent evolutionary plasticity in natural enzymes that serve as superior engineering starting points.

Active site pre-organization↗
PubMed2026

Key enzyme optimization and multi-node metabolic flux regulation drive l-arginine production in Escherichia coli.

Microbial production of l-arginine is often constrained by tight metabolic regulation and insufficient precursor supply. Here a plasmid-free, non-auxotrophic Escherichia coli strain for high-level production of l-arginine was rationally engineered, based on our previous constructed strain G0 with 12.4 g/L l-arginine production in flask. Glucose metabolism and glutamate/aspartate uptake were initially enhanced, with subsequent semi-rational engineering of key enzymes, ornithine acetyltransferase (OAT) and argininosuccinate synthase (ASS), to promote ATP synthesis. OAT was firstly rational engineered by introducing amide group for the residues near substrate-binding pocket to stabilize oxyanion transition states, with achieving that variant Y386Q showed Km/kcat at 6.58 mM-1 min-1, 2 times higher than that of wild type. Variant Y332L of ASS was novelty fused with argininosuccinate lyase via GGGGS linker for ASS activity measurement, which helped improve l-arginine titer to 17.5 g/L. With further studies by screening of rate-limiting nodes on the genome-scale level based on sRNA strategy, aspartate and glutamate pathways were synergistically enhanced, along with utilizing carbon dioxide recycling for carbamoyl phosphate synthesis to drive ammonia donor supply. The obtained final plasmid-free and non-auxotrophic strain G16 produced 21.1 g/L l-arginine in flask, 76.6% higher than that of original strain G0. In 5 L fermenter, 125.6 g/L l-arginine was produced by fed-batch fermentation, with a yield of 0.53 g/g glucose. This study underscores that the convergence of mechanistic enzyme redesign and systems-level pathway optimization is critical to unlocking high-efficient amino acid production, offering a transferable blueprint for rational strain engineering in industrial biotechnology.

Argininosuccinate synthase↗
PubMed2000

A novel method for the preparation of large cDNA fragments from dengue-3 RNA genome by long RT-PCR amplification.

For many years, dengue viruses were among the most difficult flaviviruses to isolate and to identify, but technical advances in the past 20 years have facilitated this process. Dengue viruses are usually recovered from specimens by the infection of mosquito-cell cultures. The virus may be passaged several times in cell cultures until a sufficient infectivity titer is attained. The viral nucleocapsid consists of capsid protein and an RNA genome. The dengue genome is a single stranded messenger (positive) sense RNA of approximately 11 kb in length. The isolation of dengue genomic RNA from various sources requires precautions to avoid RNases. RNases are released during cell disruption, and their activity must be inhibited as quickly as possible by using guanidinium thiocyanate in the presence of 2-mercaptoethanol. There has recently been a revolution in molecular biology with the development of the powerful reverse transcriptase (RT) and polymerase chain reaction (PCR) technology. Advanced studies on RT technique lead to much further improvement of the reverse transcriptase enzyme by genetic engineering. The Superscript II RNase H- RT (GIBCO BRL, USA) is genetically engineered DNA polymerase that synthesizes a complementary DNA strand from single-stranded RNA. DNA or an RNA-DNA hybrid. This enzyme is produced from a cloned M-MLV RT gene constructed by the introduction of point mutation in the RNase H active center. The selective mutations within the RNase H domain maintain full polymerase activity. This structural modification eliminates degradation of RNA molecules during the first strand cDNA synthesis. The combination of thermostable DNA polymerase with and without proofreading activity (3'-exonuclease activity), improved buffer conditions and thermal cycling profiles overcome the length limitation of PCR. On the basis of these findings, we have developed a long RT-PCR system for preparing large cDNA fragments of dengue 3 virus (H-87) by using the Superscript II RNase H- RT for reverse transcription and a mixture of Taq and Pwo DNA polymerases for PCR. Three large cDNA fragments covered the full genomic RNA from the 5'-end to the 3'-end of dengue-3 virus (H-87; 10,696 bps) could be successfully prepared as the lengths of 2.437 bps, 3,980 bps and 4,337 bps respectively. The ability of our developed long RT-PCR will bring speed and simplicity to genomic mapping and sequencing and facilitate studies in molecular genetics of dengue viruses.

Aedes↗
PubMed1992

Sorbitol dehydrogenase from Bacillus subtilis. Purification, characterization, and gene cloning.

Cloning of the sorbitol dehydrogenase gene (gutB) from Bacillus subtilis offers an excellent system for studying zinc binding, substrate specificity, and catalytic mechanism of this enzyme through protein engineering. As a first step to clone gutB, B. subtilis sorbitol dehydrogenase has been purified to homogeneity and characterized. It is a tetrameric enzyme with a molecular mass of 38 kDa for each subunit. Atomic absorption analysis shows the presence of 1 mol of zinc atom/subunit. Substrate specificity and stereospecificity of the enzyme toward C-2 and C-4 of hexitols were established. Sequence of the first 31 amino acids was determined, and a set of oligonucleotide probes was designed for gene cloning. A positive clone carrying a 5-kilobase pair HindIII insert was isolated and sequenced. Sequence alignment indicated that the deduced amino acid sequence of B. subtilis sorbitol dehydrogenase shows 36% identity in sequence with the liver sorbitol dehydrogenase from sheep, rat, and human. In reference to the sequence of alcohol dehydrogenase, two potential zinc binding sites were identified. Sequence information related to the structure-function relationships of the enzyme is discussed.

Amino Acid Sequence↗
PubMed1999

Recent biotechnological developments in the use of peroxidases.

Peroxidases are ubiquitous oxidoreductases that use hydrogen peroxide or alkyl peroxides as oxidants. Advances have recently been made in using them to prepare, under mild and controlled conditions, chiral organic molecules that are valuable for the chemoenzymatic synthesis of a wide range of useful compounds. Horseradish peroxidase can be converted into a peroxygenative enzyme by molecular engineering. Chloroperoxidase, the most versatile peroxidase, behaves like a 'true' monooxygenase in sulfoxidations with molecular oxygen and an external reductant, with substantial increases in enantioselectivity and enzyme stability.

Alcohols↗
PubMed1986

[New specific endonucleases PaeI and PaeII from Pseudomonas aeruginosa].

Specific endonuclease activities have been found it two Pseudomonas aeruginosa strains. Isolation and purification of enzymes and determining their specific activities have permitted one to find out that PaeI is an isoshizomer of SphI and digests the sequence 5'-GCATG C-3'. Another isolated enzyme PaeII is an isoshizomer of SmaI and cleaves DNA in a fragment 5'-CCC GGG-3'. The use of PaeI and PaeII enzymes in genetical engineering and their advantages are discussed.

Base Sequence↗
PubMed1987

Recruitment of substrate-specificity properties from one enzyme into a related one by protein engineering.

The Bacillus licheniformis and Bacillus amyloliquefaciens subtilisins differ by 31% in protein sequence and by factors of greater than 60 in catalytic efficiency, kcat/Km, toward various substrates. Despite large differences in sequence and substrate specificity for these serine proteases, only two amino acid substitutions (residues 156 and 217) occur within 4 A (contact distance) of modeled substrates, and a third substitution (residue 169) is within 7 A. The three B. licheniformis substitutions (Ser-156/Ala-169/Leu-217) were introduced into the wild-type B. amyloliquefaciens subtilisin (Glu-156/Gly-169/Tyr-217) by site-directed mutagenesis. The substrate specificity of the triple mutant approaches that of B. licheniformis enzyme when assayed with seven different substrates that vary in charge, size, and hydrophobicity. Thus, specificity properties of distantly related and functionally divergent enzymes can be exchanged by limited amino acid replacements, in this case representing less than 4% of the sequence differences.

Amino Acids↗
PubMed2003

Assessment of structural and functional divergence far from the large subunit active site of ribulose-1,5-bisphosphate carboxylase/oxygenase.

Despite conservation of three-dimensional structure and active-site residues, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1.39) enzymes from divergent species differ with respect to catalytic efficiency and CO2/O2 specificity. A deeper understanding of the structural basis for these differences may provide a rationale for engineering an improved enzyme, thereby leading to an increase in photosynthetic CO2 fixation and agricultural productivity. By comparing 500 active-site large subunit sequences from flowering plants with that of the green alga Chlamydomonas reinhardtii, a small number of residues were found to differ in regions previously shown by mutant screening to influence CO2/O2 specificity. When directed mutagenesis and chloroplast transformation were used to change Chlamydomonas Met-42 and Cys-53 to land plant Val-42 and Ala-53 in the large subunit N-terminal domain, little or no change in Rubisco catalytic properties was observed. However, changing Chlamydomonas methyl-Cys-256, Lys-258, and Ile-265 to land plant Phe-256, Arg-258, and Val-265 at the bottom of the alpha/beta-barrel active site caused a 10% decrease in CO2/O2 specificity, largely due to an 85% decrease in carboxylation catalytic efficiency (Vmax/Km). Because land plant Rubisco enzymes have greater CO2/O2 specificity than the Chlamydomonas enzyme, this group of residues must be complemented by other residues that differ between Chlamydomonas and land plants. The Rubisco x-ray crystal structures indicate that these residues may reside in a variable loop of the nuclear-encoded small subunit, more than 20 A away from the active site.

Animals↗
PubMed2005

Cell sheet engineering: recreating tissues without biodegradable scaffolds.

While tissue engineering has long been thought to possess enormous potential, conventional applications using biodegradable scaffolds have limited the field's progress, demonstrating a need for new methods. We have previously developed cell sheet engineering using temperature-responsive culture dishes in order to avoid traditional tissue engineering approaches, and their related shortcomings. Using temperature-responsive dishes, cultured cells can be harvested as intact sheets by simple temperature changes, thereby avoiding the use of proteolytic enzymes. Cell sheet engineering therefore allows for tissue regeneration by either direct transplantation of cell sheets to host tissues or the creation of three-dimensional structures via the layering of individual cell sheets. By avoiding the use of any additional materials such as carrier substrates or scaffolds, the complications associated with traditional tissue engineering approaches such as host inflammatory responses to implanted polymer materials, can be avoided. Cell sheet engineering thus presents several significant advantages and can overcome many of the problems that have previously restricted tissue engineering with biodegradable scaffolds.

Animals↗
PubMed2005

Nucleic acid enzymes.

Since the discovery of the first natural ribozyme more than 20 years ago, it has become clear that nucleic acids are not only the static depository of genetic information, but also possess intriguing catalytic activity. The number of reactions catalyzed by engineered nucleic acid enzymes is growing continuously. The versatility of these catalysts supports the idea of an ancestral world based on RNA predating the emergence of proteins, and also drives many studies towards practical applications for nucleic acid enzymes.

Catalysis↗
PubMed1989

Recent developments in enzyme and microbial biotechnology--strategies in bioprocess design.

Microorganisms have been used traditionally by industry as sources of natural products, or as sources of enzymes capable of mediating specific chemical transformations. This situation has changed radically in recent years, a time during which we have seen a dramatic increase in the number and range of potential biotechnological applications of enzymes and their genetically-engineered variants. An increasing number of enzymes, receptors and other proteins have now been structurally characterized, and their genes isolated as a basis for producing recombinant proteins for genetic analysis of their structure and function. These innovations have necessitated development of associated technologies for large-scale production of proteins in bioreactors, appropriate strategies for quality control, and new analytical tools for structural characterization of recombinant gene products. Some recombinant proteins are already in an advanced stage of development for use either as new-generation therapeutics, as target molecules for "intelligent" drug screening, or as biological components of biosensors. As the predictive power of protein model building improves, the diversity of applications of such technology will increase further as it becomes feasible to generate totally synthetic proteins with specifically-tailored properties.

Biosensing Techniques↗
PubMed2004

Biochemical characterization of the SgcA1 alpha-D-glucopyranosyl-1-phosphate thymidylyltransferase from the enediyne antitumor antibiotic C-1027 biosynthetic pathway and overexpression of sgcA1 in Streptomyces globisporus to improve C-1027 production.

Sequence analysis of the biosynthetic gene cluster for the enediyne antitumor antibiotic C-1027 from Streptomyces globisporus has previously suggested that the sgcA1 gene encodes a alpha-d-glucopyranosyl-1-phosphate thymidylyltransferase (Glc-1-P-TT) catalyzing the first step in the biosynthesis of the 4-deoxy-4-(dimethylamino)-5,5-dimethyl-d-ribopyranose moiety by activating alpha-d-glucopyranosyl-1-phosphate (Glc-1-P) into deoxythymidine diphosphate-alpha-d-glucose (dTDP-Glc). Here we report the overexpression of sgcA1 in E. coli, purification of the overproduced SgcA1 to homogenetity, biochemical and kinetic characterization of the purified SgcA1 as a Glc-1-P-TT, and yield improvement for C-1027 production by overexpression of sgcA1 and its flanking gene in S. globisporus. These findings provide biochemical evidence supporting the genetics-based hypothesis for C-1027 biosynthesis, set the stage for further investigation of the deoxysugar biosynthetic pathway, and demonstrate the utility of sugar biosynthesis genes in natural product yield improvement via combinatorial biosynthesis methods. In contrast to the homotetrameric quaternary structure known for Glc-1-P-TT enzymes from primary metabolic pathways, Glc-1-P-TT enzymes such as SgcA1 from secondary metabolic pathways are monomeric in solution. Sequence differences between the two subclasses of Glc-1-P-TT enzymes were noted. The monomeric structural feature of the latter enzymes could be exploited in engineering Glc-1-P-TT enzymes with broad substrate specificity for structural diversity via the glycorandomization strategy.

Amino Acid Sequence↗
PubMed2005

Regulation of ribozyme activity by engineered protein switch.

Previously, we showed that the P3 domain of the Escherichia coli ribonuclease P ribozyme can be truncated and replaced in vitro. In this study, we prepared a P3-replaced variant of the E. coli ribozyme that has HIV TAR sequence as the engineered P3 domain. The mutant ribozyme demonstrated the ribonuclease P activity and was inhibited in the presence of the HIV tat protein fragment. Our results showed that the P3 domain of this enzyme can be engineered, and addition of some heterologous protein subunits can also be done to this domain.

Escherichia coli Proteins↗