A searchable database for proteomes of oral microorganisms

Y. Nakano, Y. Shibata, M. Kawada, M. Kojima, H. Fukamachi, Y. Shibata, S. Okano, K. Matsushima, Y. Abiko, Y. Yamashita

研究成果: ジャーナルへの寄稿記事

8 引用 (Scopus)

抄録

An online database of proteomes for two-dimensional electrophoresis (2DE) gel data was constructed and it is now freely accessible through a web-based interface. Proteins from three oral bacteria, Streptococcus mutans UA159, Actinobacillus actinomycetemcomitans HK1651, and Porphyromonas gingivalis W83, whose genome databases are freely available, were separated by 2DE, and protein spots were analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and identified. About 1000 spots from the gels of P. gingivalis W83 were extracted and analyzed by MALDI-TOF, and 330 proteins were identified. In addition, 160 of 240 spots of A. actinomycetemcomitans and 158 of 356 spots of S. mutans were identified. Information such as spot coordinates on the gels, protein names (predicted functions), molecular weights, isoelectroric points, and links to online databases, including Oral Pathogen Sequence Databases of the Los Alamos National Laboratory Bioscience Division (ORALGEN) and National Center for Biotechnology Information (NCBI) or The Institute Genomic Research (TIGR), were stored in tables accessible through the relational database management system MySQL on an Apache web server. To test for functionality of this database system, responses of S. mutans to environmental changes were analyzed using the database and 21 spots on the gel were identified as proteins whose expression had been increased or decreased by environmental pH change without in-gel trypsin digestion, protein extraction, or MALDI-TOF/TOF-MS (mass spectrometer) analysis. The identified proteins are agreement with those reported in previous papers on acid tolerance of S. mutans, demonstrating the usefulness of the system.

元の言語英語
ページ(範囲)344-348
ページ数5
ジャーナルOral Microbiology and Immunology
20
発行部数6
DOI
出版物ステータス出版済み - 12 1 2005

Fingerprint

Proteome
Streptococcus mutans
Databases
Gels
Aggregatibacter actinomycetemcomitans
Porphyromonas gingivalis
Proteins
Lasers
Database Management Systems
Information Centers
Electrophoresis, Gel, Two-Dimensional
Biotechnology
Trypsin
Proteolysis
Names
Molecular Weight
Genome
Bacteria
Acids

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Immunology
  • Dentistry(all)
  • Microbiology (medical)

これを引用

A searchable database for proteomes of oral microorganisms. / Nakano, Y.; Shibata, Y.; Kawada, M.; Kojima, M.; Fukamachi, H.; Shibata, Y.; Okano, S.; Matsushima, K.; Abiko, Y.; Yamashita, Y.

:: Oral Microbiology and Immunology, 巻 20, 番号 6, 01.12.2005, p. 344-348.

研究成果: ジャーナルへの寄稿記事

Nakano, Y, Shibata, Y, Kawada, M, Kojima, M, Fukamachi, H, Shibata, Y, Okano, S, Matsushima, K, Abiko, Y & Yamashita, Y 2005, 'A searchable database for proteomes of oral microorganisms', Oral Microbiology and Immunology, 巻. 20, 番号 6, pp. 344-348. https://doi.org/10.1111/j.1399-302X.2005.00235.x
Nakano, Y. ; Shibata, Y. ; Kawada, M. ; Kojima, M. ; Fukamachi, H. ; Shibata, Y. ; Okano, S. ; Matsushima, K. ; Abiko, Y. ; Yamashita, Y. / A searchable database for proteomes of oral microorganisms. :: Oral Microbiology and Immunology. 2005 ; 巻 20, 番号 6. pp. 344-348.
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