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I Endo

Publications and source records attributed to I Endo.

At least 19 recordsLinked to original sources
PubMed1996

Gene for aspartate racemase from the sulfur-dependent hyperthermophilic archaeum, Desulfurococcus strain SY.

Amino acid racemases are ubiquitous throughout eubacteria. However, no amino acid racemases have yet been found in eukaryotes and archaea. We cloned a gene highly homologous to that for the aspartate racemase from the sulfur-dependent hyperthermophilic archaeum, Desulfurococcus strain SY. The product of the gene showed 35.2% amino acid sequence identity with the aspartate racemase of Streptococcus thermophilus IAM10064, and was also homologous to glutamate racemases around the putative catalytic cysteine residues. The encoded protein was expressed in Escherichia coli. The recombinant protein had amino acid racemizing activity, which was highly specific for aspartate and increased with temperature from 37 degrees C to 90 degrees C. Therefore, this was identified as the first hyperthermophilic archaeal amino acid racemase. A little aspartate racemizing activity was also detected in the crude extract of Desulfurococcus strain SY. The function of this aspartate racemase might be the uptake of -aspartate formed at high temperature or the production of -aspartate as a cell component. The fact that the amino acid racemases are distributed among both eubacteria and archaea suggests that endogenous -amino acids in mammals are also synthesized by amino acid racemases.

Amino Acid Isomerases↗
PubMed1996

A novel factor required for the assembly of the DnaK and DnaJ chaperones of Thermus thermophilus.

We previously reported the isolation of T.DnaK.DnaJ chaperone complex from Thermus thermophilus. Here, we show that a novel factor is necessary for the assembly of T.DnaK and T.DnaJ into the complex. A dnaK gene cluster of T. thermophilus contained five genes, dnaK-grpE-dnaJ-orf4-clpB. Interestingly, T.DnaJ lacks the whole "cysteine-rich region" that has been postulated to be necessary to bind unfolded proteins. The orf4 gene encodes a novel 78-amino acid protein. Curiously, T.DnaK and T.DnaJ expressed in Escherichia coli did not form the complex. Careful reexamination of the T.DnaK.DnaJ complex revealed the presence of a small protein in the complex, which turned out to be a product of orf4. As expected, expression of three genes, dnaK-dnaJ-orf4, resulted in production of a T.DnaK.DnaJ complex in E. coli that was indistinguishable from the authentic complex in its ability to interact with nucleotide and denatured protein. The product of orf4 was also required for in vitro reconstitution of the complex and named T.DafA (T.DnaK.DnaJ assembly factor A). The complex comprises three copies each of T.DnaK, T.DnaJ, and T.DafA. Even though a definite homolog of T.DafA has not been found in the data base, this finding raises a possibility that interaction between DnaK and DnaJ chaperones in other organisms is also mediated by a small protein yet unnoticed.

Amino Acid Sequence↗
PubMed1996

Location of the non-heme iron center on the alpha subunit of photoreactive nitrile hydratase from Rhodococcus sp. N-771.

Nitrile hydratase (NHase) from Rhodococcus sp. N-771, which possesses a non-heme iron center binding nitric oxide (NO), is activated by light irradiation. To localize the iron center in the protein, we quantified Fe atoms and performed FTIR measurements of the isolated alpha and beta subunits. The native NHase and the isolated alpha subunit contained about 1.0 and 0.8 mol Fe per mol protein, respectively, whereas the beta subunit contained only a trace of Fe. An NO stretching band was observed at 1852 cm-1 in the FTIR spectrum of the alpha subunit, but not in that of the beta subunit. Upon light irradiation of the alpha subunit, the affinity of the Fe atom decreased and the NO band disappeared from the FTIR spectrum. These observations indicate that the non-heme iron center, which is responsible for the photoreaction, is present in the alpha subunit.

Amino Acid Sequence↗
PubMed1996

Photoreactive nitrile hydratase: the photoreaction site is located on the alpha subunit.

Nitrile hydratase (NHase) from Rhodococcus sp. N-771 exists in active and inactive forms. The inactive NHase is immediately activated by light irradiation and changes to the active form. To characterize the photoreactive center, the inactive NHase was denatured by 6 M urea, and two kinds of subunits (alpha and beta) were separated and purified by anion-exchange chromatography. In a manner similar to the native NHase, the isolated alpha subunit showed two absorption peaks at 280 and 370 nm, which were diminished by light irradiation. However, irradiation failed to elicit the appearance of absorption peaks at around 400 nm and at 710 nm, which were characteristic of the activated enzyme. The beta subunit seemed not to possess any photoreactive chromophore because its absorption spectrum was not altered by light irradiation. Neither of the subunits showed NHase activity before and after light irradiation, but the inactive NHase was reconstituted by incubating the two subunits together in the dark at 4 degrees C for 1 h. Light irradiation of the beta subunit did not affect subsequent complex formation or NHase activity. However, the irradiated alpha subunit could not assemble with the beta subunit, and no activity was recovered. These results demonstrate that the chromophore(s) responsible for the photoactivation of NHase are entirely located on the alpha subunit, and imply that light irradiation induces conformational change of the alpha subunit.

Binding Sites↗
PubMed1995

Gene of heat shock protein of sulfur-dependent archaeal hyperthermophile Desulfurococcus.

To elucidate thermoresistance, a gene of a hyperthermophilic heat shock protein (HHSP) was isolated from the hyperthermophile Desulfurococcus strain SY which grows at 95 degrees C. The molecular weight of HHSP deduced from the open reading frame was 59,137 (545 amino acid residues). Sequence alignments of peptides reveal similarities (evolutionary distances) to the alpha (0.279) and beta (0.296) subunits of thermosome, TF55 (0.343) and human t-complex polypeptide 1. The structure of a thermophilic heat shock protein TGroEL (Tamada et al. (1991) Biochem, Biophys. Res. Commun. 179, 565) was quite different from that of HHSP. TGroEL and HSP60 have sequences identical to HHSP at its equatorial domain, while those identical to the alpha subunit of F-type ATPase are at its apical domain.

Amino Acid Sequence↗
PubMed1995

Solid-phase nested deletion: a new subcloning-less method for generating nested deletions.

We have developed a new subcloning-less method for generating nested deletions which we have termed Solid-Phase Nested Deletion. The basic procedure for this method is as follows. The target DNA fragment is cloned in the multiple cloning site of a cloning vector, pUC or its derivatives, and amplified by PCR using a set of primers, one of which is 5'-biotinylated. The amplified DNA is partially digested by a restriction enzyme with a 4-base recognition sequence. The digested DNA is ligated with a synthetic adapter DNA. Monodiverse beads coupled with streptavidin (Dynabeads M-280 streptavidin) are added to the mixture and the biotinylated DNA fragments are separated by applying magnetic field. The unidirectionally deleted DNA fragments are recovered by PCR from the magnetic beads, and size-fractionated by agarose gel electrophoresis. The DNA fragments are amplified by PCR and used for sequencing. We demonstrate the potential of this method using a 4878-bp EcoRI fragment of lambda phage DNA.

Bacteriophage lambda↗
PubMed1995

Photosensitive nitrile hydratase intrinsically possesses nitric oxide bound to the non-heme iron center: evidence by Fourier transform infrared spectroscopy.

Nitrile hydratase (NHase) from Rhodococcus sp. N-771 is a photosensitive enzyme that catalyzes hydration of nitriles to the corresponding amides. Light-induced Fourier transform infrared difference spectra between the inactive and active forms of NHase were measured with both the natural (14N) and 15N-labeled NHases. The results showed, for the first time, that NHase intrinsically possesses nitric oxide (NO) molecules bound to the non-heme iron center. The possible role of NO in the photoactivation process of NHase is discussed.

Enzyme Activation↗
PubMed1995

Molecular cloning, expression, and characterization of chaperonin-60 and chaperonin-10 from a thermophilic bacterium, Thermus thermophilus HB8.

The gene coding a chaperonin from a thermophilic bacterium, Thermus thermophilus HB8, was cloned and sequenced. The operon structure was the same as those of other bacterial chaperonins and the deduced amino acid sequences of both subunits were highly homologous to those of other chaperonins. The cloned genes of chaperonin subunits, chaperonin-10 (T.th cpn10) and chaperonin-60 (T.th cpn60), were separately expressed in Escherichia coli cells. The expressed subunits were easily purified from other host proteins including GroE, a chaperonin of E. coli. T.th cpn60 was expressed as a tetradecameric form, like GroEL of E. coli. Since chaperonin from T. thermophilus HB8 is purified as a holochaperonin, a complex of tetradecameric T.th cpn60 and heptameric T.th cpn10, a tetradecamer of T.th cpn60 without T.th cpn10 has not been obtained before. T.th cpn60 tetradecamer tended to dissociate into monomers during storage. T.th cpn10 expressed in E. coli was purified as a stable oligomer, most likely a heptamer. The activity as holo-chaperonin was reconstituted by mixing both subunits. T.th cpn60 tetradecamer itself arrested refolding of other proteins. The monomerized T.th cpn60 was easily purified from T.th cpn60 oligomer by gel permeation chromatography. Thus-obtained T.th cpn60 monomer had an ATP-independent chaperone activity, as shown for T.th cpn60 monomer isolated from authentic holo-chaperonin.

3-Isopropylmalate Dehydrogenase↗
PubMed1994

Effects of linear polyacrylamide concentrations and applied voltages on the separation of oligonucleotides and DNA sequencing fragments by capillary electrophoresis.

Oligonucleotides and DNA sequencing fragments have been separated by capillary electrophoresis employing linear polyacrylamide (LPA) as a sieving matrix. A commercially available apparatus equipped with a laser-induced fluorescence (LIF) detection system has been utilized, but the capillary cartridge has been modified to position the capillaries without coiling. The performance of the separation, the relationship between resolution and analysis time, has been examined using poly(dT)16-500 by changing LPA concentration, capillary length, and electric field strength. It was found that, for large DNA fragments, the migration time interval between bands decreases linearly as DNA fragment size increases. This implies that there exists a maximum base number to be resolved, irrespective of the band width (we named the maximum base number Nmax). The higher value of Nmax is obtained when the applied field strength is lower, but this accompanies longer analysis time with a concomitant increase in band width. Simple experimental equations have been proposed to calculate resolution and migration times of DNA fragments separated in our system at given electrophoretic conditions. Using 9% T LPA and an electric field strength of 100 V/cm, single-base resolution of M13mp10 DNA fragments up to 520 nucleotides has been obtained.

Acrylic Resins↗
PubMed1994

Spectroscopic observation of the intramolecular electron transfer in the photoactivation processes of nitrile hydratase.

The photoactivation phenomena of the photosensitive enzyme nitrile hydratase (NHase) was studied by various spectroscopic methods. We have already shown that the photoactivation of NHase accompanies oxidation of an iron atom in the NHase [Honda et al. (1992) FEBS Lett. 301, 177-180]. From the results obtained in the present study by absorption, action, and fluorescence spectra, we show that the chromophore responsible for the photoactivation process is the iron complex, and the tryptophan residues in NHase induce the oxidation of the iron atom via an energy-transfer process. The nanosecond flash photolysis experiment revealed that this photoactivation process is completed within 50 ns, which suggests that the changes observable in the absorption spectra originate from an intramolecular electron transfer occurring from an electronically excited state. Also the role of a stabilizing reagent, namely, n-butyric acid (BA), was investigated using the above methods, which revealed that BA, besides its stabilizing effect, contributes to the increase in apparent photoactivation rate.

Butyrates↗
PubMed1994

High speed polymerase chain reaction in constant flow.

A new simple reactor of the tubing type was developed for polymerase chain reaction (PCR). A thin Teflon capillary tube was used as a tubing reactor in which the reaction mixture of PCR was driven by a pump at a constant flow rate. The sample was treated with three successive thermal stages for denaturation, annealing, and elongation of DNA and primers as a function of the position in the tube. The amplification yield was about a half of that obtained by a commercial thermocycler. Moreover, the total reaction time from 12 to 18 min, which was one-tenth of the time generally required by conventional thermocyclers using metal blocks, assured substaintial amplification of a DNA fragment. In addition, this reactor could be also used for rapid cycle-sequences. This new device will be easily incorporated into automated and rapid DNA analysis systems for DNA sequencing.

Base Sequence↗
PubMed1994

Role of nuclear histone-H1 kinase in regeneration of rat liver.

The activities of nuclear histone-H1 kinase and C-kinase as well as the amount of phosphate bound to histone-H1 following partial hepatectomy were studied in rat. It was found that the nuclear histone-H1 kinase activity increased twice within 80 h, first 20 to 30 h, and second at 50 to 70 h after partial hepatectomy. The timing of increase of the enzyme activity correlated with increased amount of bound phosphate. On the other hand, the increase of the C-kinase activities occurred between 5 and 15 h after partial hepatectomy. Antibodies raised against human cdk2, human cyclin-A and mouse cdc2 kinase showed no detectable effect on the nuclear histone H1 kinase activity. These results suggest that phosphorylation of histone-H1 in liver regeneration may be catalysed by a putative kinase(s).

Animals↗
PubMed1992

Light-induced oxidation of iron atoms in a photosensitive nitrile hydratase.

The photoactivation process of a photosensitive nitrile hydratase (NHase) from Rhodococcus sp. N-771 has been investigated by 57Fe Mössbauer spectroscopy and magnetic susceptibility measurements in order to clarify the behavior of iron atoms in the enzyme. Mössbauer spectra of inactive NHase gave two symmetric-doublet components indicating the presence of two iron species, while that of the active NHase gave a single symmetric doublet indicating the presence of a single iron species. Magnetic susceptibility measurements of the inactive and active HNase both showed small effective magnetic moments. These results led us to conclude that one of the two iron atoms incorporated in the NHase is oxidized during photoactivation, namely from a low spin ferrous to a low spin ferric state. This is the first observation of an intramolecular photooxidation phenomena involving iron in a single protein molecule.

Enzyme Activation↗
PubMed1992

Object-oriented fuzzy expert system for on-line diagnosing and control of bioprocesses.

An object-oriented fuzzy expert system to support on-line control of an automated fermentation plant is described. The major elements of the system consist of a fuzzy inference engine, a database, a knowledge base, and an expression evaluater. The expression evaluater calculates specific rates for growth, and substrate and product formation at different physiological states during the cultivation from the measured data. The specific rates are then compared with the standard target rates stored in the database. If differences outside the set tolerances were observed, the inference engine analyses the reasons for the faults on the basis of the knowledge represented in the form of a knowledge network and fuzzy membership functions of the process variables. The fuzzy expert system was developed on the basis of a shell constructed by using the object oriented Smalltalk/V Mac programming environment, with Lac-tobacillus casei lactic acid fermentation as the example of process application.

Biotechnology↗