Kaoru Nakasone - Academia.edu (original) (raw)

Papers by Kaoru Nakasone

Microbiology resource announcements, Aug 18, 2022

Saccharomyces cerevisiae strain DJJ01 was isolated from Dojoji Temple (Gobo, Wakayama, Japan) for... more Saccharomyces cerevisiae strain DJJ01 was isolated from Dojoji Temple (Gobo, Wakayama, Japan) for development of local breweries. Here, we report the draft genome sequence of this strain to facilitate comparative genomic studies of yeast strains used for Japanese sake brewing.

We have cloned and sequenced the ftsZ gene, encoding a protein essential for cell division, from ... more We have cloned and sequenced the ftsZ gene, encoding a protein essential for cell division, from a 1 phage library of the chromosome of the deep-sea bacterium Shewanella violacea strain DSS12. This gene, 1,179 bp in length, was found to encode a protein consisting of 392 amino acid residues with a molecular mass of 40,727 Da. Significant homology was evident comparing the ItsZ gene of S. violacea with that of Escherichia coli(63% identity), Pseudomonas putida (51% identity), Bacillus subtilis (48% identity), and Streptomyces coelicolor(43% identity). Comparison of the amino acid sequences of the FtsZ proteins of S. violacea and E. coli revealed the presence of a GTPase domain in N-terminal portion and a specific conserved region in the C-terminal portion (extreme C-terminus) which is associated with other cell division proteins. A variable region between the GTPase domain and the C-terminal region was also observed.

The Japanese Biochemical Society/The Molecular Biology Society of Japan, Oct 23, 2017

Molecular BioSystems, 2010

We have cloned and sequenced the endA gene, encoding deoxyribonuclease, from a λ phage library of... more We have cloned and sequenced the endA gene, encoding deoxyribonuclease, from a λ phage library of the chromosome of the deep-sea bacterium Shewanella violacea strain DSS. This gene, bp in length, was found to encode a protein consisting of amino acid residues with a molecular mass of , Da. Significant homology was evident comparing the endA gene of S. violacea with that of V. vulnificus (% identity), S. typhimurium (% identity), E. chrysanthemi (% identity) and E. coli (% identity). Phylogenetic analyses of EndA proteins of several bacteria showed that S. violacea is closely related to V. vulnificus. Expression plasmid to overproduce the EndA protein was also constructed.

Proceedings of International Symposium on Extremophiles and Their Applications International Symposium on Extremophiles and Their Applications 2005, 2007

Dna Sequence, Feb 1, 2005

The rpoE gene encoding an RNA polymerase sigmaE subunit was isolated from a gamma-phage library o... more The rpoE gene encoding an RNA polymerase sigmaE subunit was isolated from a gamma-phage library of the deep-sea piezophilic and psychrophilic bacterium Shewanella violacea strain DSS12. Structual analysis showed that the gene organization of the fragment containing S. violacearpoE was the l-aspartate oxidase-coding gene, rpoE, rseA, rseB and rseC in that order, the same as in the case of Photobacterium profundum SS9 and Escherichia coli K-12. The cloned gene, 576 bp in length, was found to encode a protein consisting of 192 amino acid residues with a molecular mass of 21,806 Da. Amino acid alignment of the RpoE protein showed that the functional domains responsible for DNA recognition, DNA melting, core binding, and RseA interaction were highly conserved. We purified hexahistidine-fused RpoE protein by constructing an overexpression plasmid. Core-binding analysis revealed that the cloned RpoE protein has the ability to bind with core RNA polymerase as a sigma factor.

70 subunits of eubacterial counterpart. The molecular masses of these subunits were 30,000, 152,0... more 70 subunits of eubacterial counterpart. The molecular masses of these subunits were 30,000, 152,000, 162,000, 82,000 Da, respectively as measured by SDSPAGE. An in vitro transcription assay using the RNAI promoter as a transcription template revealed that the enzyme of S. violacea initiated transcription at the same site as that of Escherichia coli.

日本生物工学会大会講演要旨集, Aug 25, 2011

Bioscience, Biotechnology, and Biochemistry, 2000

Biochimica et biophysica acta (N), Apr 1, 2000

We have recently reported that a σ54-like factor recognizes a DNA element, designated as region A... more We have recently reported that a σ54-like factor recognizes a DNA element, designated as region A, upstream of a pressure-regulated operon in piezophilic Shewanella violacea strain DSS12 (Nakasone et al., FEMS Microbiology Lett. 176 (1999) 351–356). In this study, we isolated and characterized the rpoN gene of this piezophilic bacterium. The rpoN gene was found to encode a putative protein consisting of 492 amino acid residues with a predicted molecular mass of 55 359 Da. Significant homology was evident comparing the rpoN sequence of S. violacea with that of Escherichia coli (62.8% identity), Vibrio anguillarum (61.7% identity) and Pseudomonas putida (57.0% identity). The DNA-binding domain at the C-terminus of σ54 is well conserved in the case of the S. violacearpoN gene product and the helix-turn-helix motif and the RpoN box are also present. In addition, the conserved glutamine-rich domain is present at the N-terminus. σ54 in S. violacea was expressed at a relatively constant level under various growth conditions as determined by both primer extension and Western blotting analyses. By means of a recombinant plasmid, a hexahistidine-tagged derivative of the σ54 from strain DSS12 was overexpressed in Escherichia coli and purified to near homogeneity. An electrophoretic mobility shift assay demonstrated that the purified σ54 protein specifically recognizes region A in the above-mentioned pressure-regulated operon.

Dna Sequence, Apr 1, 2004

ABSTRACT We have cloned the rpoZ gene, encoding RNA polymerase ω protein, by PCR approach from th... more ABSTRACT We have cloned the rpoZ gene, encoding RNA polymerase ω protein, by PCR approach from the deep-sea piezophilic and psychrophilic bacterium, Shewanella violacea strain DSS12. The cloned gene, 285 bp in length, was found to encode a protein consisting of 94 amino acid residues with a molecular mass of 10,327 Da. Significant homology was evident comparing the RpoZ protein of S. violacea with that of Shewanella oneidensis (69% identity), Vibrio cholerae (65% identity), Escherichia coli K-12 (64% identity) and Haemophilus influenzae (61% identity). From the Northern blot analysis, S. violacea rpoZ gene was expressed constitutively under pressure conditions of 0.1, 30 and 50 MPa. We constructed expression plasmid to overproduce the RpoZ protein and transformed into E. coli JM109 as a host of overproduction. Upon induction, the recombinant protein encoded by plasmid pQrpoZ was overexpressed and purified using Ni2+ affinity column.

Journal of Bacteriology, May 15, 2000

Two c-type cytochromes from the soluble fraction of a deep-sea moderately piezophilic bacterium, ... more Two c-type cytochromes from the soluble fraction of a deep-sea moderately piezophilic bacterium, Shewanella violacea, were purified and characterized, and the genes coding for these cytochromes were cloned and sequenced. One of the cytochromes, designated cytochrome c A , was found to have a molecular mass of approximately 8.3 kDa, and it contained one heme c per molecule. The other, designated cytochrome c B , was found to have a molecular mass of approximately 23 kDa, and it contained two heme c molecules per protein molecule. The amount of cytochrome c B expressed in cells grown at high hydrostatic pressure (50 MPa) was less than that in cells grown at atmospheric pressure, whereas cytochrome c A was constitutively expressed under all pressure conditions examined. The results of Northern blotting analysis were consistent with the above-mentioned observations and suggested that the pressure regulation of cytochrome c B gene expression occurred at the transcriptional level. These results suggest that the components of the respiratory chain of moderately piezophilic S. violacea could be exchanged according to the growth pressure conditions.