Biomedical subjects

I Urabe

Publications and source records attributed to I Urabe.

At least 19 recordsLinked to original sources

PubMed2001

Plasticity of fitness and diversification process during an experimental molecular evolution.

A simplified experimental evolution encompassing the essence of natural one was designed in an attempt to understand the involved mechanism. In our system, molecular evolution was observed through three serial cycles of consecutive random mutagenesis of the glutamine synthetase gene and chemostat culture of the transformed Escherichia coli cells containing the mutated genes. Selection pressure was imposed solely on the glutamine synthetase gene when varieties of mutant genes compete in an unstructured environment of the chemostat. The molecular phylogeny and population dynamics were deduced from the nucleotide sequences of the genes isolated from each of the chemostat runs. An initial mutant population in each cycle, comprised of diversified closely-related genes, ended up with several varieties of mutants in a state of coexistence. Competition between two mutant genes in the final population of the first cycle ascertained that the observed coexisting state is not an incidental event and that cellular interaction via environmental nutrients is a possible mechanism of coexistence. In addition, the mutant gene once extinct in the previous passage was found to have the capacity to reinvade and constitute the gene pool of the later cycle of molecular evolution. These results, including the kinetic characteristics of the purified wild-type and mutant glutamine synthetases in the phylogenetic tree, revealed that the enzyme activity had diverged, rather than optimized, to a fittest value during the course of evolution. Here, we proposed that the plasticity of gene fitness in consequence of cellular interaction via the environment is an essential mechanism governing molecular evolution.

Escherichia coli↗

PubMed2001

Crystal structure of glucose dehydrogenase from Bacillus megaterium IWG3 at 1.7 A resolution.

The crystal structure of glucose dehydrogenase (GlcDH) from Bacillus megaterium IWG3 has been determined to an R-factor of 17.9% at 1.7 A resolution. The enzyme consists of four identical subunits, which are similar to those of other short-chain reductases/dehydrogenases (SDRs) in their overall folding and subunit architecture, although cofactor binding sites and subunit interactions differ. Whereas a pair of basic residues is well conserved among NADP(+)-preferring SDRs, only Arg39 was found around the adenine ribose moiety of GlcDH. This suggests that one basic amino acid is enough to determine the coenzyme specificity. The four subunits are interrelated by three mutually perpendicular diad axes (P, Q, and R). While subunit interactions through the P-axis for GlcDH are not so different from those of the other SDRs, those through the Q-axis differ significantly. GlcDH was found to have weaker hydrophobic interactions in the Q-interface. Moreover, GlcDH lacks the salt bridge that stabilizes the subunit interaction in the Q-interface in the other SDRs. Hydrogen bonds between Q-axis related subunits are also less common than in the other SDRs. The GlcDH tetramer dissociates into inactive monomers at pH 9.0, which can be attributed mainly to the weakness of the Q-axis interface.

Amino Acid Sequence↗

PubMed2001

Effects of amino acid substitution on the physicochemical properties of artificial proteins with random sequences.

Physicochemical properties of four random proteins, each consisting of about 150 amino acid residues with different sequence identity, were compared to know the correlation between the physicochemical properties and its sequence. The results showed that the extent of the sequence alterations correlated well with the extent of differences in CD spectra, roughly with those in pH-solubility profiles and sedimentation velocity, and not with that in the binding of a hydrophobic fluorescent dye (ANS). Therefore, proteins with similar sequences can have different physicochemical properties, indicating that the extent of mutational effects varies in response to the sequence being altered. This warrants the evolution of a protein in a sequence-specific manner.

Journal Article↗

PubMed2001

Synthesis of functional protein in liposome.

The liposome consisting of eggPC, cholesterol, and DSPE-PEG5000 with a molar ratio of 1.5:1:0.08 was used to entrap cell-free protein synthesis reaction mixture. The synthesis of a mutant green fluorescent protein in the liposome was confirmed by the fluorescence emitted from the liposome on flow cytometry analysis and fluorescence microscopy. The protein synthesized in the liposome is hence functional.

Journal Article↗

PubMed2000

Construction and characterization of phage libraries displaying artificial proteins with random sequences.

Three phage libraries, PL1, PL2, and PL3, displaying artificial proteins with random sequences were constructed. The artificial proteins, which are model of ancestral proteins, are derivatives of the 25 kinds of random proteins with about 140 amino acid residues produced via random mutagenesis and combinatorial recombination. The random proteins were displayed on the surface of filamentous bacteriophage as fusion protein with the pIII coat protein at an estimated average number on the phage particles in PL1, PL2, and PL3 of 0.32, 0.32, and 0.08, respectively. Each library was shown to express 10(5) to 10(6) kinds of random proteins. With the phage libraries displaying long random peptides, we now have an effective selection system to observe in vitro evolution of new functional proteins from artificial proteins with random sequences.

Journal Article↗

PubMed2000

Crystallization and preliminary X-ray analysis of glucose dehydrogenase from Bacillus megaterium IWG3.

Glucose dehydrogenase from Bacillus megaterium IWG3 has been crystallized in the presence of NAD(+) using the hanging-drop vapour-diffusion method with PEG 2000 as the precipitant. Crystals belong to space group C2 and have unit-cell parameters a = 120.8 (1), b = 66.7 (1), c = 119.6 (1) A, beta = 93.25 (3) degrees with standard deviations in parentheses. Assumption of four subunits in the asymmetric unit gave the most probable Matthews coefficient V(M) of 2.1 A(3) Da(-1) (solvent content 41.7% by volume). X-ray diffraction data were collected to 1.7 A on a synchrotron-radiation source.

Bacillus megaterium↗

PubMed2000

Physical properties of the dentin-enamel junction region.

PURPOSE: To determine the physical properties between enamel and dentin at the dentin-enamel junction (DEJ) region of natural tooth structure. MATERIALS AND METHODS: Ultimate tensile cohesive strengths of the DEJ region of human and bovine teeth were measured using a microtensile test, and the nanohardness and Young's modulus from deep enamel to superficial dentin of human teeth were measured using a nanoindentation tester. RESULTS: The mean ultimate tensile cohesive strengths of bovine and human DEJ region were 47.7 MPa and 51.5 MPa, respectively. The nanohardness, dynamic hardness and Young's modulus of the DEJ region showed moderate values between those of enamel and dentin. Comparison of the cohesive strength of the human DEJ region with previous results of the bond strength of resin bonding systems indicate that current resin bonding systems might reproduce the biological adhesion of enamel to dentin in terms of the tensile strength. Moreover, the indentation properties of the DEJ region showed higher values than those of the underlying dentin or of resin impregnated dentin.

Acid Etching, Dental↗

PubMed1999

Evolutionary molecular engineering by random elongation mutagenesis.

We describe a new method of random mutagenesis that employs the addition of peptide tails with random sequences to the C-terminal of enzyme molecules. A mutant population of catalase I from Bacillus stearothermophilus prepared by this method has a diversity in thermostability and enzyme activity equal to that obtained after random point mutagenesis. When a triple mutant of catalase I (I108T/D130N/1222T)-the thermostability of which is much lower than that of the wild type-was subjected to random elongation mutagenesis, we generated a mutant population containing only mutants with higher thermostability than the triple mutant. Some had an even higher stability than the wild-type enzyme, whose thermostability is considered to be optimized. These results indicate that peptide addition expands the protein sequence space resulting in a new fitness landscape. The enzyme can then move along the routes of the new landscape until it reaches a new optimum. The combination of random elongation mutagenesis with random point mutagenesis should be a useful approach to the in vitro evolution of proteins with new properties.

Amino Acid Sequence↗

PubMed1998

Properties of artificial proteins with random sequences.

A library of artificial proteins of 141 amino acid residues, of which 95 are random and which include 20 kinds of amino acids, was prepared. As the properties of the artificial random proteins are free from the evolutionary constraint, they can be used as a standard to discriminate the specialized properties of natural proteins. Out of the 25 identified random proteins, 5 are soluble in the cell lysate, indicating that about 20% of the random proteins expressed in Escherichia coli are expected to be soluble. Therefore, as natural soluble or insoluble proteins can arise from the line of soluble or insoluble ancestry, respectively, solubility does not seem a specialized property of natural proteins. The soluble random proteins RP3-42 and RP3-45 were purified and their properties were investigated.

Amino Acid Sequence↗

PubMed1998

Characterization of soluble artificial proteins with random sequences.

The structural and catalytic properties of two soluble random proteins, RP3-42 and RP3-45, of 141 amino acid residues were investigated. Although no marked secondary structure was detected by CD spectrum, sedimentation equilibrium and small-angle X-ray scattering studies showed that they form an oligomeric structure and are as compact as the molten globule. The random proteins have low but distinct esterase activity; the values of the second-order rate constant for the hydrolysis of p-nitrophenol were 0.78 and 1.39 M(-1) s(-1) for RP3-42 and RP3-45, respectively. The differences in the properties of the random and the native proteins are discussed from the evolutionary point of view.

Amino Acid Sequence↗

PubMed1998

Nonadditivity of mutational effects on the properties of catalase I and its application to efficient directed evolution.

Catalase I of Bacillus stearothermophilus has high catalatic and low peroxidatic activities. The mutant from the first random mutant population, D130N, which has higher peroxidatic and lower catalatic activities than those exhibited by the wild-type enzyme, was subjected to second random mutagenesis in observance of the change in reaction specificity. From the second mutant population, the mutant I108T/D130N/I222T was selected and examined. The reaction specificity of the purified enzymes revealed that catalase I being originally 98% catalase and 2% peroxidase was brought to 58% specificity to peroxidase after two-step adaptive walks. From the statistical analysis of the two random mutant populations, the average degree of nonadditivity of the mutational effects was estimated to be 0.13 irrespective of the properties of the enzyme. It was demonstrated that the distribution pattern of a property of the second mutant population can be predicted well from the data of the first mutant population by taking into consideration the degree of nonadditivity. The strategy for an efficient adaptive walk in directed evolution of enzymes through the prediction of appropriate mutation rate and effective sample size for further mutation and selection was presented and discussed.

Catalase↗

PubMed1998

Escherichia coli transformant expressing the glucose dehydrogenase gene from Bacillus megaterium as a cofactor regenerator in a chiral alcohol production system.

Escherichia coli JM109 (pGDA2) overexpressing the glucose dehydrogenase (GDH) gene from Bacillus megaterium IWG3 was examined for use as a cofactor regenerator. In the asymmetric reduction of ethyl 4-chloro-3-oxobutanoate by E. coli JM109 (pKAR) which is an aldehyde reductase-overproducing transformant, E. coli JM109 (pGDA2) can act as an NADPH regenerator with NADP+ and glucose, similarly to commercially available GDH.

Alcohols↗

PubMed1997

General equation of steady-state enzyme kinetics using net rate constants and its applicaiton to the kinetic analysis of catalase reaction.

The steady-state velocity equation is derived for the general reaction scheme containing n kinds of enzyme species connected by a network of reversible reaction steps. The general equation is represented by the net rate constants as well as the true rate constants of the individual reaction steps. Using a general equation, equations for simpler schemes can easily be derived. Furthermore, the velocity equation expressed by net rate constants is useful for understanding the dynamic state of any reaction be it simple or complex. The generality of the presented equation is tested in a complex reaction involving Bacillus stearothermophilus catalase I. In addition, the applicability of the general equation in analysing the reaction specificity and dynamic state of the reaction is shown.

Animals↗

PubMed1997

Thermal conversion from low- to high-activity forms of catalase I from Bacillus stearothermophilus.

Catalase I from Bacillus stearothermophilus has the interesting property of increasing its enzyme activity on heating. It was confirmed that after heating at 70 degrees C for 10 min or 65 degrees C for 20 min, almost all the enzyme molecules were converted irreversibly to the activated form. The increase in kcat from 1400 to 3930 s-1 and the decrease in Km for H2O2 from 4.4 to 2.7 mM by heat activation indicate changes in the kinetic property of the enzyme molecule. Therefore, it follows that catalase I has two active forms, a high-activity form and a low-activity form. The heat activation process followed the first-order kinetics with an activation enthalpy (DeltaH*) of 191 kJ/mol while the heat denaturation process had a DeltaH* of 545 kJ/mol. The CD spectra of the two enzyme forms had small but marked differences. The conversion of the low-activity form to the high-activity form was an endothermic process with a Tm of 56 degrees C, which is much lower than that of the heat denaturation (Tm = 76 degrees C), and the enthalpy change for the transition was only 5% of that for the denaturation. It has to be noted that the high-activity form of the enzyme was converted back to a low-activity form through the process of denaturation, refolding, and reconstitution with heme. In addition, the newly obtained low-activity form was brought to a high-activity form by heating. These results suggest that the native state of catalase I has two active conformations that are roughly the same but not identical and are separated by a high energy barrier.

Calorimetry, Differential Scanning↗

PubMed1996

Application of N-terminally truncated DNA polymerase from Thermus thermophilus (delta Tth polymerase) to DNA sequencing and polymerase chain reactions: comparative study of delta Tth and wild-type Tth polymerases.

N-Terminally truncated DNA polymerase from Thermus thermophilus (delta Tth polymerase) lacking 5'-3' exonuclease activity was used for DNA sequencing and polymerase chain reaction (PCR). In contrast to the high background of the sequencing ladder observed with the wild-type Tth polymerase, delta Tth polymerase gave readable sequencing patterns which extend up to more than 500 bases from the primer site on cycle sequencing and automated sequencing. The delta Tth polymerase was used for the standard and mutagenic PCR, and net amplification of the DNA and the mutations accumulated during PCR were analyzed. Under mutagenic PCR, the mutation rates were 7.0 x 10(-4) (Tth) and 8.3 x 10(-4) (delta Tth) per nucleotide per cycle of amplification, which were 4-9 times higher than the rates under standard PCR.

Automation↗

PubMed1996

Solubility of artificial proteins with random sequences.

A library of artificial random proteins of 141 amino acid residues of which 95 are random and which includes the 20 kinds of amino acids was prepared. Out of the 25 identified random proteins, 5 were soluble in the cell lysate, indicating that about 20% of the random proteins expressed in Escherichia coli are expected to be soluble. The soluble random proteins RP3-42 and RP3-45 and insoluble RP3-70 were purified. The solubility of the purified form is the same as that in the cell lysate.

Amino Acid Sequence↗

PubMed1995

A plasmid encoding enzymes for nylon oligomer degradation: nucleotide sequence and analysis of pOAD2.

The entire nucleotide sequence of nylon oligomer degradative plasmid pOAD2 from Flavobacterium sp. KI723T1 was determined. pOAD2 comprises 45519 bp, with a 66.6 mol% G+C content. The precise loci of the four nylon oligomer degradation genes, namely nylA (6-aminohexanoate-cyclic-dimer hydrolase gene), nylB (6-aminohexanoate-dimer hydrolase), nylB' (a gene having 88% homology to nylB) and nylC (endo-type 6-aminohexanoate oligomer hydrolase), and five IS6100 elements were identified on this plasmid. Comparison of the sequence of pOAD2 with those in the GenBank and EMBL databases revealed that the deduced amino acid sequences from eight regions of pOAD2 had significant similarity with the sequences of gene products such as oppA-F (oligopeptide permeases), ftsX (filamentation temperature sensitive), penDE (isopenicillin N-acyltransferase) and rep (plasmid incompatibility). A functional map of pOAD2 is presented.

Amidohydrolases↗

PubMed1995

Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution.

Through selective cultivation with 6-aminohexanoate linear dimer, a by-product of nylon-6 manufacture, as the sole source of carbon and nitrogen, Pseudomonas aeruginosa PAO, which initially has no enzyme activity to degrade this xenobiotic compound, was successfully expanded in its metabolic ability. Two new enzyme activities, 6-aminohexanoate cyclic dimer hydrolase and 6-aminohexanoate dimer hydrolase, were detected in the adapted strains.

Amidohydrolases↗