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At least 217 records · Page 12Linked to original sources
PubMed2006

Analysis of novel soluble chromate and uranyl reductases and generation of an improved enzyme by directed evolution.

Most polluted sites contain mixed waste. This is especially true of the U.S. Department of Energy (DOE) waste sites which hold a complex mixture of heavy metals, radionuclides, and organic solvents. In such environments enzymes that can remediate multiple pollutants are advantageous. We report here evolution of an enzyme, ChrR6 (formerly referred to as Y6), which shows a markedly enhanced capacity for remediating two of the most serious and prevalent DOE contaminants, chromate and uranyl. ChrR6 is a soluble enzyme and reduces chromate and uranyl intracellularly. Thus, the reduced product is at least partially sequestered and nucleated, minimizing the chances of reoxidation. Only one amino acid change, (Tyr)128(Asn), was responsible for the observed improvement. We show here that ChrR6 makes Pseudomonas putida and Escherichia coli more efficient agents for bioremediation if the cellular permeability barrier to the metals is decreased.

Directed Molecular Evolution↗
PubMed1976

Enzyme recruitment in evolution of new function.

Ancient cells must have possessed small gene content. Primitive enzymes may have possessed broad specificity and undeveloped regulation mechanisms. The considerable substrate ambiguity of these enzymes resulted in the formation of minor amounts of erroneous products. Fortuitous formation of metabolites offered ancient cells maximum biochemical flexibility with minimal gene content. Gene duplication provided the opportunity for increased gene content and increased specialization of the diverging enzymes, the substrate specialization being further reinforced by the development of regualtory mechanisms. Recuritment of enzymes for new pathways did not necessarily require the sequential and backwardly evolving progression of evolutionary steps required by the hypothesis of retrograde evolution of biochemical pathways. Substrate ambiguity remains a conspicuous feature of many contemporary proteins, and evolutionary exploitation of substrate ambiguity in a variety of organisms is still apparent.

Amino Acids↗
PubMed1988

The perfection of substrate-channelling in interacting enzyme systems: energetics and evolution.

Some implications of substrate channelling in interacting enzyme systems are considered, with regard to the energetics and evolution of enzyme action. The transient time, a key analytical parameter relating to the phenomenon of channelling, is the basis of our kinetic study. Bounds on the kinetics of multienzyme complexes are established using (apparent) rate constants emanating from the transient-time formulation of coupled reactions. From a transition state representation of the rate process, it is shown how dynamically and statically organized enzyme systems lead to the modification of current ideas on the evolutionary optimization of the energy profile of enzyme catalysis in situ.

Biological Evolution↗
PubMed2005

Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design.

Many research groups successfully rely on whole-gene random mutagenesis and recombination approaches for the directed evolution of enzymes. Recent advances in enzyme engineering have used a combination of these random methods of directed evolution with elements of rational enzyme modification to successfully by-pass certain limitations of both directed evolution and rational design. Semi-rational approaches that target multiple, specific residues to mutate on the basis of prior structural or functional knowledge create 'smart' libraries that are more likely to yield positive results. Efficient sampling of mutations likely to affect enzyme function has been conducted both experimentally and, on a much greater scale, computationally, with remarkable improvements in substrate selectivity and specificity and in the de novo design of enzyme activities within scaffolds of known structure.

Combinatorial Chemistry Techniques↗
PubMed2003

Functional cooperation between exonucleases and endonucleases--basis for the evolution of restriction enzymes.

Many types of restriction enzymes cleave DNA away from their recognition site. Using the type III restriction enzyme, EcoP15I, which cleaves DNA 25-27 bp away from its recognition site, we provide evidence to show that an intact recognition site on the cleaved DNA sequesters the restriction enzyme and decreases the effective concentration of the enzyme. EcoP15I restriction enzyme is shown here to perform only a single round of DNA cleavage. Significantly, we show that an exonuclease activity is essential for EcoP15I restriction enzyme to perform multiple rounds of DNA cleavage. This observation may hold true for all restriction enzymes cleaving DNA sufficiently far away from their recognition site. Our results highlight the importance of functional cooperation in the modulation of enzyme activity. Based on results presented here and other data on well-characterised restriction enzymes, a functional evolutionary hierarchy of restriction enzymes is discussed.

Binding Sites↗
PubMed1992

Alterations in mRNA translation as a mechanism for the modification of enzyme synthesis during evolution. The ornithine decarboxylase model.

The expression of renal ornithine decarboxylase (ODC) is very different between the two murine species Mus domesticus and Mus pahari. The latter species contains a reduced level of ODC protein in the kidney, yet a normal concentration of ODC mRNA, indicating an alteration in translation, protein degradation, or both. We describe two lines of experimental evidence indicating that the efficiency of ODC mRNA translation is decreased in M. pahari. First, in vivo measurements showed that the rate of biosynthesis of the ODC polypeptide is reduced in M. pahari relative to M. domesticus. Second, polysome analyses indicated that, on average, the ODC mRNA of M. pahari binds fewer ribosomes. These effects, which are kidney-specific, lend support to the notion that renal ODC expression in the two species differs at the level of mRNA translation. A full-length cDNA copy of the ODC mRNA of M. pahari was isolated, and its sequence was compared with that of M. domesticus. In the 5'-untranslated region, which is likely to play an important role in controlling translation, the M. pahari transcript contains several single-base changes, as well as a 12-base deletion. These changes confer a distinct predicted secondary structure to this region of the mRNA and may be involved in reduced translation. We conclude that during evolution, modifications that alter the biosynthesis of specific proteins can occur at the translational level; these modifications exert their effects on translation in a transcript- and tissue-specific manner.

Amino Acid Sequence↗
PubMed2005

Rational genomics I: antisense open reading frames and codon bias in short-chain oxido reductase enzymes and the evolution of the genetic code.

The short-chain oxidoreductase (SCOR) family of enzymes includes over 6000 members, extending from bacteria and archaea to humans. Nucleic acid sequence analysis reveals that significant numbers of these genes are remarkably free of stopcodons in reading frames other than the coding frame, including those on the antisense strand. The genes from this subset also use almost entirely the GC-rich half of the 64 codons. Analysis of a million hypothetical genes having random nucleotide composition shows that the percentage of SCOR genes having multiple open reading frames exceeds random by a factor of as much as 1 x 10(6). Nevertheless, screening the content of the SWISS-PROT TrEMBL database reveals that 15% of all genes contain multiple open reading frames. The SCOR genes having multiple open reading frames and a GC-rich coding bias exhibit a similar GC bias in the nucleotide triple composition of their DNA. This bias is not correlated with the GC content of the species in which the SCOR genes are found. One possible explanation for the conservation of multiple open reading frames and extreme bias in nucleic acid composition in the family of Rossman folds is that the primordial member of this family was encoded early using only very stable GC-rich DNA and that evolution proceeded with extremely limited introduction of any codons having two or more adenine or thymine nucleotides. These and other data suggest that the SCOR family of enzymes may even have diverged from a common ancestor before most of the AT-rich half of the genetic code was fully defined.

Amino Acid Sequence↗
PubMed2003

The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: co-evolution of structure and dynamics with the dehalogenation function.

Bacterial muconate lactonizing enzymes (MLEs) catalyze the conversion of cis,cis-muconate as a part of the beta-ketoadipate pathway, and some MLEs are also able to dehalogenate chlorinated muconates (Cl-MLEs). The basis for the Cl-MLEs dehalogenating activity is still unclear. To further elucidate the differences between MLEs and Cl-MLEs, we have solved the structure of Pseudomonas P51 Cl-MLE at 1.95 A resolution. Comparison of Pseudomonas MLE and Cl-MLE structures reveals the presence of a large cavity in the Cl-MLEs. The cavity may be related to conformational changes on substrate binding in Cl-MLEs, at Gly52. Site-directed mutagenesis on Pseudomonas MLE core positions to the equivalent Cl-MLE residues showed that the variant Thr52Gly was rather inactive, whereas the Thr52Gly-Phe103Ser variant had regained part of the activity. These residues form a hydrogen bond in the Cl-MLEs. The Cl-MLE structure, as a result of the Thr-to-Gly change, is more flexible than MLE: As a mobile loop closes over the active site, a conformational change at Gly52 is observed in Cl-MLEs. The loose packing and structural motions in Cl-MLE may be required for the rotation of the lactone ring in the active site necessary for the dehalogenating activity of Cl-MLEs. Furthermore, we also suggest that differences in the active site mobile loop sequence between MLEs and Cl-MLEs result in lower active site polarity in Cl-MLEs, possibly affecting catalysis. These changes could result in slower product release from Cl-MLEs and make it a better enzyme for dehalogenation of substrate.

Amino Acid Sequence↗
PubMed2004

Understanding the importance of protein structure to nature's routes for divergent evolution in TIM barrel enzymes.

It is widely agreed that new enzymes evolve from existing ones through the duplication of genes encoding existing enzymes followed by sequence divergence. While evolution is an inherently random process, studies of divergently related enzymes have shown that the evolution of new enzymes follows one of three general routes in which the substrate specificity, reaction mechanism, or active site architecture of the progenitor enzyme is reused in the new enzyme. Recent developments in structural biology relating to divergently related (beta/alpha)8 enzymes have brought new insight into these processes and have revealed that conserved structural elements play an important role in divergent evolution. These studies have shown that, although evolution occurs as a series of random mutations, stable folds such as the (beta/alpha)8 barrel and structural features of the active sites of enzymes are frequently reused in evolution and adapted for new catalytic purposes.

Binding Sites↗
PubMed2004

Directed evolution of protein enzymes using nonhomologous random recombination.

We recently reported the development of nonhomologous random recombination (NRR) as a method for nucleic acid diversification and applied NRR to the evolution of DNA aptamers. Here, we describe a modified method, protein NRR, that enables proteins to access diversity previously difficult or impossible to generate. We investigated the structural plasticity of protein folds and the ability of helical motifs to function in different contexts by applying protein NRR and in vivo selection to the evolution of chorismate mutase (CM) enzymes. Functional CM mutants evolved using protein NRR contained many insertions, deletions, and rearrangements. The distribution of these changes was not random but clustered in certain regions of the protein. Topologically rearranged but functional enzymes also emerged from these studies, indicating that multiple connectivities can accommodate a functional CM active site and demonstrating the ability to generate new domain connectivities through protein NRR. Protein NRR was also used to randomly recombine CM and fumarase, an unrelated but also alpha-helical protein. Whereas the resulting library contained fumarase fragments in many contexts before functional selection, library members surviving selection for CM activity invariably contained a CM core with fumarase sequences found only at the termini or in one loop. These results imply that internal helical fragments cannot be swapped between these proteins without the loss of nearly all CM activity. Our findings suggest that protein NRR will be useful in probing the functional requirements of enzymes and in the creation of new protein topologies.

Chorismate Mutase↗
PubMed1984

Evolution of proteolytic enzymes.

Proteolytic enzymes have many physiological functions, ranging from generalized protein digestion to more specific regulated processes such as the activation of zymogens, blood coagulation and the lysis of fibrin clots, the release of hormones and pharmacologically active peptides from precursor proteins, and the transport of secretory proteins across membranes. They are present in all forms of living organisms. Comparisons of amino acid sequences, three-dimensional structures, and enzymatic reaction mechanisms of proteases indicate that there are distinct families of these proteins. Changes in molecular structure and function have accompanied the evolution of proteolytic enzymes and their inhibitors, each having relatively simple roles in primitive organisms and more diverse and more complex functions in higher organisms.

Amino Acid Sequence↗
PubMed2004

Discovery of pectin-degrading enzymes and directed evolution of a novel pectate lyase for processing cotton fabric.

There is a growing need in the textile industry for more economical and environmentally responsible approaches to improve the scouring process as part of the pretreatment of cotton fabric. Enzymatic methods using pectin-degrading enzymes are potentially valuable candidates in this effort because they could reduce the amount of toxic alkaline chemicals currently used. Using high throughput screening of complex environmental DNA libraries more than 40 novel microbial pectate lyases were discovered, and their enzymatic properties were characterized. Several candidate enzymes were found that possessed pH optima and specific activities on pectic material in cotton fibers compatible with their use in the scouring process. However, none exhibited the desired temperature characteristics. Therefore, a candidate enzyme was selected for evolution. Using Gene Site Saturation Mutagenesistrade mark technology, 36 single site mutants exhibiting improved thermotolerance were produced. A combinatorial library derived from the 12 best performing single site mutants was then generated by using Gene Reassemblytrade mark technology. Nineteen variants with further improved thermotolerance were produced. These variants were tested for both improved thermotolerance and performance in the bioscouring application. The best performing variant (CO14) contained eight mutations and had a melting temperature 16 degrees C higher than the wild type enzyme while retaining the same specific activity at 50 degrees C. Optimal temperature of the evolved enzyme was 70 degrees C, which is 20 degrees C higher than the wild type. Scouring results obtained with the evolved enzyme were significantly better than the results obtained with chemical scouring, making it possible to replace the conventional and environmentally harmful chemical scouring process.

Bacteria↗
PubMed2003

Directed evolution of industrial enzymes: an update.

The use of enzymes in industrial processes can often eliminate the use of high temperatures, organic solvents and extremes of pH, while at the same time offering increased reaction specificity, product purity and reduced environmental impact. The growing use of industrial enzymes is dependent on constant innovation to improve performance and reduce cost. This innovation is driven by a rapidly increasing database of natural enzyme diversity, recombinant DNA and fermentation technologies that allow this diversity to be produced at low cost, and protein modification tools that enable enzymes to be tuned to fit into the industrial marketplace.

6-Phytase↗
PubMed1982

Angiotensin converting enzyme activity and evolution of pulmonary vascular disease in rats with monocrotaline pulmonary hypertension.

We have investigated the role of angiotensin converting enzyme (ACE) in the development of pulmonary hypertension, right ventricular hypertrophy, and pulmonary vascular disease in rats given a single subcutaneous injection of the pyrrolizidine alkaloid monocrotaline. Thirty-six young female Wistar rats were divided into a test group of 27 animals and a control group of nine animals. Each test rat was given a single subcutaneous injection of monocrotaline (60 mg/kg body weight). On the first, third, fifth, seventh, tenth, twelfth, fourteenth, seventeenth, and twenty-second days after the injection of monocrotaline the mean right ventricular systolic blood pressure was measured in one control and three test rats. The animals were then killed and we measured the specific activity of ACE in serum and lung homogenate. We also evaluated muscularisation of pulmonary arterioles, medial hypertrophy of muscular pulmonary arteries, and right ventricular hypertrophy. The sequence of changes was as follows: muscularisation of pulmonary arterioles and medial hypertrophy of muscular pulmonary arteries were apparent seven days after administration of monocrotaline; pulmonary hypertension and reduced lung ACE activity occurred after 10 days; right ventricular hypertrophy was detected after 12 days. Serum ACE activity was unchanged. It is concluded that the reduction in lung ACE activity is a result rather than a cause of the pulmonary hypertension. This reduction in lung ACE activity may be a protective mechanism designed to limit the elevation of the pulmonary arterial pressure.

Animals↗
PubMed1998

Directed evolution of new enzymes and pathways for environmental biocatalysis.

Biocatalysis is important in both natural and engineered environments. The major global reactions in the biospheric cycling of carbon, nitrogen, and other elements are catalyzed by microorganisms. The global carbon cycle includes millions of organic compounds that are made by plants, microorganisms, and organic chemists. Most of those compounds are transformed by microbial enzymes. Degradative metabolism is known as catabolism and yields principally carbon dioxide, methane, or biomass. Microbial catabolic enzymes are a great resource for biotechnology. They are the building blocks for engineering novel metabolic pathways and evolving improved enzymes in the laboratory. Two multicomponent bacterial oxygeneases, cytochrome P450cam and toluene dioxygenase, catalyze the dechlorination of polyhalogenated C2 compounds. Seven genes encoding those functional enzyme complexes were coexpressed in a Pseudomonas and shown to metabolize pentachloreothane to nonhalogenated organic acids that were metabolized further to carbon dioxide. In another example, the enzyme catalyzing the dechlorination of the herbicide atrazine was subjected to iterative DNA shuffling to produce mutations. By using a plate screening assay, mutated atrazine chlorohydrolase that catalyzed a more rapid dechlorination of atrazine was obtained. The mutant genes were sequences and found to encode up to 11 amino acid changes. Atrazine chlorohydrolase is currently being used in a model municipal water treatment system to test the feasibility of using enzymes for atrazine decontamination. These data suggest that the natural diversity of bacterial catabolic enzymes provides the starting point for improved biocatalytic systems that meet the needs of commercial applications.

Biodegradation, Environmental↗
PubMed1995

Polymorphism in the 3' untranslated region of the phenylalanine hydroxylase gene detected by enzyme mismatch cleavage: evolution of haplotypes.

A polymorphism was identified in 3' untranslated region of the phenylalanine hydroxylase gene using the newly described mutation detection method, enzyme mismatch cleavage. This polymorphism, 1546 G-->A, was linked to three mutations on several haplotype backgrounds. A group of haplotypes was identified as evolving from the one ancestral haplotype on which this base substitution occurred. The possible Celtic or Viking origin of this polymorphism is discussed.

Base Sequence↗
PubMed2003

Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution.

Yeast cytosine deaminase is an attractive candidate for anticancer gene therapy because it catalyzes the deamination of the prodrug 5-fluorocytosine to form 5-fluorouracil. We report here the crystal structure of the enzyme in complex with the inhibitor 2-hydroxypyrimidine at 1.6-A resolution. The protein forms a tightly packed dimer with an extensive interface of 1450 A2 per monomer. The inhibitor was converted into a hydrated adduct as a transition-state analog. The essential zinc ion is ligated by the 4-hydroxyl group of the inhibitor together with His62, Cys91, and Cys94 from the protein. The enzyme shares similar active-site architecture to cytidine deaminases and an unusually high structural homology to 5-aminoimidazole-4-carboxamide-ribonucleotide transformylase and thereby may define a new superfamily. The unique C-terminal tail is involved in substrate specificity and also functions as a gate controlling access to the active site. The complex structure reveals a closed conformation, suggesting that substrate binding seals the active-site entrance so that the catalytic groups are sequestered from solvent. A comparison of the crystal structures of the bacterial and fungal cytosine deaminases provides an elegant example of convergent evolution, where starting from unrelated ancestral proteins, the same metal-assisted deamination is achieved through opposite chiral intermediates within distinctly different active sites.

Amino Acid Sequence↗