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Biomedical subjects

K Horikoshi

Publications and source records attributed to K Horikoshi.

At least 109 records · Page 6Linked to original sources
PubMed1996

Isolation and characterization of the gene encoding an aminopeptidase involved in the selective toxicity of ascamycin toward Xanthomonas campestris pv. citri.

An aminopeptidase gene named XAP has been isolated from Xanthomonas campestris pv. citri, a plant pathogenic bacterium. The bacterium is one of the rare micro-organisms susceptible to ascamycin, an aminoacyl nucleoside antibiotic that inhibits protein synthesis. Sequence analysis reveals that the gene encodes a 311 amino acid protein with a calculated molecular mass of 35134 Da and approx. 50% identity for amino acids to the proline iminopeptidase from Neisseria gonorrhoeae. The XAP gene product, Xap, expressed in Escherichia coli has proline iminopeptidase activity as well as ascamycin dealanylating activity in vitro.

Adenosine↗
PubMed1996

Molecular cloning of the gene encoding RNA polymerase alpha subunit from deep-sea barophilic bacterium.

We have cloned the gene encoding RNA polymerase alpha subunit from a gene library of deep-sea barophilic bacterium strain DB6705. The clone contains the genes for ribosomal protein S4, RNA polymerase subunit alpha and ribosomal protein L17 in this order. The alpha gene has 328 amino acids and a molecular mass of 36 100 Da with 86.9% identity to Escherichia coli alpha gene. Differences between the two sequences were mainly in the N-terminal portion of the alpha subunit, which is involved in the assembly of the core RNA polymerase; while the 87 C-terminal residues, which form a region involved in contact with some positive regulators and rrnB P1 promoter region called UP-element, were identical in the both strain. Plasmid encoding the alpha subunit with an N-terminal hexahistidine tag was constructed. Using the plasmid, the recombinant fusion alpha subunit was overexpressed and successfully purified to near homogeneity.

Amino Acid Sequence↗
PubMed1996

Culturability and survival of an extreme thermophile isolated from deep-sea hydrothermal vents

The culturability of a strictly anaerobic, extremely thermophilic archaeon, Thermococcus peptonophilus (optimal growth temperature: 85° C), was studied during survival stages at various temperatures (98, 85, 70, and 4° C). Total cell number (determined by DAPI staining), active cells (rhodamine-stained cells), and culturable cells (using most-probable-number) were counted over time. The number of culturable cells decreased under each condition tested. The total number of cells significantly decreased only at temperatures close to the maximum for growth (98° C); at this temperature, the cells spontaneously lysed. Our results suggested that survival at 4° C in oxygenated waters might be a mechanism for the dispersion of extreme thermophiles in the ocean. In addition, we proved the existence of T. peptonophilus cells in several physiological states: culturable cells, active non-culturable cells, inactive non-culturable cells, and dead cells. Cell death was caused by cellular lysis.

Journal Article↗
PubMed1996

Characterization of malate dehydrogenase from deep-sea psychrophilic Vibrio sp. strain no. 5710 and cloning of its gene.

A metabolic key enzyme malate dehydrogenase (MDH) was purified from a deep-sea psychrophilic bacterium, Vibrio sp. strain no. 5710. The enzyme displayed an optimal activity shifted toward lower temperature and a pronounced heat lability. A gene encoding this enzyme was isolated and cloned. Recombinant Escherichia coli cells harboring the isolated clone expressed MDH activity with temperature stability identical to that of the parental psychrophile. Nucleotide sequencing of the gene revealed that its primary sequence was similar to that of a mesophile E. coli MDH (78% amino acid identity), for which the three-dimensional structure is known. The enzyme is thus suitable for the analysis of molecular adaptations to low temperatures.

Adaptation, Physiological↗
PubMed1996

High pressure represses expression of the malB operon in Escherichia coli.

The formation of plaques by lambda phage in Escherichia coli was prevented by elevated hydrostatic pressure; phage plaques were not detected at 30 MPa. Furthermore, using promoter fragments derived from the malB operon, we showed that gene expression initiated from both promoters (malK-lamB and malEFG) was repressed by elevated hydrostatic pressure. Our findings suggest that high pressure affects gene expression directed by the malB regulatory interval, and this may cause a decrease in the quantities of lambda receptor protein, LamB.

Atmospheric Pressure↗
PubMed1996

Isolating and characterizing deep-sea marine microorganisms.

We have isolated several microorganisms that are adapted to living in the extremes of the deep-sea environment. They include barophilic bacteria, which are able to grow at high hydrostatic pressure, but that are unable to grow at atmospheric pressure, and organic-solvent-tolerant bacteria, which are able to grow in the presence of toxic organic solvents such as toluene or benzene. In this review, we describe how to isolate such extremophiles, and we outline the characteristics of several strains that have been recovered from the deep-sea environment.

Bacteria↗
PubMed1996

Open reading frame 3 of the barotolerant bacterium strain DSS12 is complementary with cydD in Escherichia coli: cydD functions are required for cell stability at high pressure.

Escherichia coli strain JD518, a cydD-deficient mutant, displayed temperature-sensitive and pressure-sensitive growth. The defective cydD gene in this strain was complemented by open reading frame 3 (ORF3), previously identified in DNA from a barotolerant bacterium, strain DSS12, allowing growth of the cydD mutant under high temperature and high pressure conditions. Spectrophotometrical analysis indicated that the cytochrome bd complex which is assembled by the CydD protein was expressed in E. coli strain JD518 carrying the ORF3 gene at the same level as occurred in the wild-type strain. Our results indicate that the cydD gene functions are required for cell stability under the condition of high pressure stress in bacteria.

ATP-Binding Cassette Transporters↗
PubMed1996

Diversity of Nitrogen Fixation Genes in the Symbiotic Intestinal Microflora of the Termite Reticulitermes speratus.

The diversity of nitrogen-fixing organisms in the symbiotic intestinal microflora of a lower termite, Reticulitermes speratus, was investigated without culturing the resident microorganisms. Fragments of the nifH gene, which encodes the dinitrogenase reductase, were directly amplified from the DNA of the mixed microbial population in the termite gut and were clonally isolated. The phylogenetic analysis of the nifH product amino acid sequences showed that there was a remarkable diversity of nitrogenase genes in the termite gut. A large number of the termite nifH sequences were most closely related to those of a firmicute, Clostridium pasteurianum, with a few being most closely related to either the (gamma) subclass of the proteobacteria or a sequence of Desulfovibrio gigas. Some of the others were distantly related to those of the bacteria and were seemingly derived from the domain Archaea. The phylogenetic positions of these nifH sequences corresponded to those of genera found during a previous determination of rRNA-based phylogeny of the termite intestinal microbial community, of which a majority consisted of new, yet-uncultivated species. The results revealed that we have little knowledge of the organisms responsible for nitrogen fixation in termites.

Journal Article↗
PubMed1996

A novel member of the cspA family of genes that is induced by cold shock in Escherichia coli.

Escherichia coli contains a major cold shock protein, CspA (or CS7.4), whose production is predominantly induced at low temperatures. This bacterium is known to possess five additional genes, each encoding a protein highly similar to CspA (referred to as the CspA family). Here we identified a gene that encodes a cold-shock-inducible analog of CspA and CspB. This newly cloned cspG gene is located at 22 min on the E. coli genetic map, apart from the other cspA family genes. Its gene product (70 amino acids) is 73 and 77% identical to CspA (70 amino acids) and CspB (71 amino acids), respectively. Analyses of a cspG-lacZ transcriptional fusion and Northern (RNA) hybridization revealed that cspG is a low-temperature-responsive gene. Its low-temperature-inducible promoters were determined, and the results indicated that the cspG sequence is highly similar to both the cspA and cspB sequences not only in the coding regions but also in the 5'-upstream noncoding regions surrounding their own promoters.

Amino Acid Sequence↗
PubMed1995

Phylogeny of symbiotic methanogens in the gut of the termite Reticulitermes speratus.

The phylogeny of a symbiotic methanogen inhabiting the gut of a lower termite. Reticulitermes speratus, was analysed without cultivation. The small subunit ribosomal RNA gene (ssrDNA) and a 640-bp portion of the gene encoding subunit A of methyl coenzyme M reductase (mcrA) were amplified from a mixed-population DNA of the termite gut by polymerase chain reaction and cloned. The nucleotide sequence of the ssrDNA and the predicted amino acid sequence of the mcrA product were compared with those of the known methanogens. Both comparisons indicated that the termite symbiotic methanogen belonged to the order Methanobacteriales but was distinct from the known members of this order.

Animals↗
PubMed1995

Hydrostatic pressure promotes the acidification of vacuoles in Saccharomyces cerevisiae.

Application of hydrostatic pressure caused a delay or cessation of cell growth in Saccharomyces cerevisiae. The yeast vacuole is an acidic organelle involved in cellular ion homeostasis and degradation of proteins. Hydrostatic pressure promoted the acidification of the vacuoles in the strain IFO 2347. A pressure of 40 to 60 MPa reduced the vacuolar pH, defined using 6-carboxyfluorescein, from 6.05 to 5.88, while a pressure of 20 MPa did not affect the pH. Similar results were obtained with the strain X2180. Bafilomycin A1, a specific inhibitor of vacuolar H(+)-ATPase (V-H(+)-ATPase), caused a significant alkalization of vacuoles in the strain X2180. The pHs rose to 7.34 and 6.84 at both atmospheric pressure and a pressure of 40 MPa, respectively. Meanwhile, vacuolar accumulation of the weak base quinacrine was increased by a pressure of 40 MPa, suggesting that uptake of the dye was induced by the increased pH gradient across the vacuolar membrane.

Anti-Bacterial Agents↗
PubMed1995

High pressure influences on gene and protein expression.

Elevated hydrostatic pressure can influence gene and protein expression in both 1 atmosphere-adapted and high pressure-adapted microorganisms. Here we review experiments documenting these effects and describe their significance towards understanding the molecular bases of life in deep-sea high pressure environments.

Bacterial Proteins↗
PubMed1995

Properties of glutamate dehydrogenase and its involvement in alanine production in a hyperthermophilic archaeon, Thermococcus profundus.

Thermococcus profundus, a hyperthermophilic archaeon, did not exhibit detectable glutamine synthetase activity, although the organism possessed an extraordinarily high level of glutamate dehydrogenase (GDH), the content of which reached over 10% of total soluble proteins. This GDH was purified to homogeneity. The enzyme had a molecular weight of 263,000 and was composed of six homogeneous subunits of molecular weight 43,000. The enzyme was extremely thermostable with a half life of 1 h at 90 degrees C. Circular dichroism (CD) spectra of the enzyme revealed gradual unfolding of alpha-helices upon exposure to increasing temperature. The enzyme reaction was strongly biased toward glutamate formation. T. profundus excreted L-alanine into the medium, and the concentration reached mM. High activity of alanine aminotransferase (AAT) was present in the cells, while no alanine dehydrogenase activity was detected. The alanine formation may be initiated by ammonia uptake by GDH followed by aminotransfer from glutamate to pyruvate by AAT.

Alanine↗
PubMed1995

Degradation of polyaromatic hydrocarbons by organic solvent-tolerant bacteria from deep sea.

We isolated three organic solvent (OS)-tolerant bacterial strains DS-1051, DS-1902, and DS-313 from a depth of 1,168 m in Sagami Bay, Japan. These isolates were tolerant to various kinds of toxic OSs such as benzene, toluene, and p-xylene. They also could degrade polyaromatic hydrocarbons, naphthalene or biphenyl, in a medium-OS (9:1) two-liquid-phase system. Percentage degradation of polyaromatic hydrocarbons in OS by these strains were higher than those obtained from cultures in which substrates were in the medium without OS.

Bacteria↗
PubMed1995

Effect of hydrostatic pressure on the synthesis of outer membrane proteins in Escherichia coli.

We examined the effects of hydrostatic pressure on the synthesis of Escherichia coli outer membrane proteins, particularly for the osmoregulated ImpC and OmpF porins. It was found that the expression of ompC and ompF was markedly reduced during the growth at high pressure, most likely at the transcriptional level. However, the signal transduction processes through the regulatory proteins, EnvZ and OmpR, was not influenced by the environmental pressure. It was also found that the expression of a presumed novel outer membrane protein, named OmpX, was affected by both the medium osmolarity and pressure in a manner independent of the function of EnvZ and OmpR.

Bacterial Outer Membrane Proteins↗
PubMed1995

Characterization of a mutation responsible for an alkali-sensitive mutant, 18224, of alkaliphilic Bacillus sp. strain C-125.

An alkali-sensitive mutant, 18224, of the alkaliphilic Bacillus sp. strain C-125 was characterized. The nucleotide sequence of the PvuI-NlaIV DNA fragment that recovers the alkaliphily of 18224 has been cloned from the mutant and sequenced. Comparison of the nucleotide sequences of the corresponding regions found a G to A substitution in the mutant. The mutation resulted in an amino acid substitution from 82Gly to Glu of the putative ORF3 product, which consisted a gene cluster of at least four tandemly located open reading frames. The ORF3 product was deduced to be an 112 amino acid polypeptide with hydrophobic properties, which was expressed using an in vitro translation system.

Alkalies↗
PubMed1995

A hyperthermophilic sulfur-reducing archaebacterium, Thermococcus sp. DT1331, isolated from a deep-sea hydrothermal vent.

A hyperthermophilic archaebacterium was isolated from a deep-sea black smoker chimney (depth, 760 m) at the Minami-ensei Knoll (28 degrees 23'N, 127 degrees 38'E). The strain, designated DT1331, was a coccoid shaped bacterium about 0.5 to 1.0 microns in diameter. The cells were surrounded by a cell envelope. The temperature for growth was between 55 degrees C and 93 degrees C with an optimum 80 degrees C. The growth occurred from pH 4.5 to 8.5 and the optimum pH was 6.0. DT1331 required 1% to 5% NaCl for growth and cell lysis was observed below 1% NaCl concentration. The strain was an anaerobic chemoorganotroph requiring elemental sulfur obligately. Organic substrates used included tryptone, peptone, soytone, casein, gelatin, and yeast extract. Under the optimal conditions, DT1331 had a generation time of 50 min and could reach densities of about 1.5 x 10(8) cells/ml. DT1331 was resistant to ampicillin, chloramphenicol, erythromycin, kanamycin, streptomycin, and tetracycline, which was one of the common characteristics of archaebacteria. The G+C content of DT1331 was 52.3 mol%. Analysis of the 16S rRNA gene by restriction enzymes coincided with those of Thermococcus celer, indicating that this strain belonged to the genus Thermococcus.

Anti-Bacterial Agents↗