'98 Escherichia coli SWISS-2DPAGE database update

Luisa Tonella*, Brad J. Walsh, Jean Charles Sanchez, Keli Ou, Marc R. Wilkins, Margaret Tyler, Séverine Frutiger, Andrew A. Gooley, Ioana Pescaru, Ron D. Appel, Jun X. Yan, Amos Bairoch, Christine Hoogland, Fabienne S. Morch, Graham J. Hughes, Keith L. Williams, Denis F. Hochstrasser

*Corresponding author for this work

Research output: Contribution to journalArticle

85 Citations (Scopus)

Abstract

The combination of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), computer image analysis and several protein identification techniques allowed the Escherichia coli SWISS-2DPAGE database to be established. This is part of the ExPASy molecular biology server accessible through the WWW at the URL address http://www.expasy.ch/ch2d/ch2d-top.html. Here we report recent progress in the development of the E. coli SWISS- 2DPAGE data-base. Proteins were separated with immobilized pH gradients in the first dimension and sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. To increase the resolution of the separation and thus the number of identified proteins, a variety of wide and narrow range immobilized pH gradients were used in the first dimension. Micropreparative gels were electroblotted onto polyvinylidene difluoride membranes and spots were visualized by amido black staining. Protein identification techniques such as amino acid composition analysis, gel comparison and microsequencing were used, as well as a recently described Edman 'sequence tag' approach. Some of the above identification techniques were coupled with database searching tools. Currently 231 polypeptides are identified on the E. coli SWISS-2DPAGE map: 64 have been identified by N- terminal microsequencing, 39 by amino acid composition, and 82 by sequence tag. Of 153 proteins putatively identified by gel comparison, 65 have been confirmed. Many proteins have been identified using more than one technique. Faster progress in the E. coli proteome project will now be possible with advances in biochemical methodology and with the completion of the entire E. coli genome.

Original languageEnglish
Pages (from-to)1960-1971
Number of pages12
JournalElectrophoresis
Volume19
Issue number11
DOIs
Publication statusPublished - Aug 1998

Keywords

  • immobilized pH gradient
  • sequence tag
  • SWISS-2DPAGE database
  • two-dimensional polyacrylamide gel electrophoresis Escherichia coli

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    Tonella, L., Walsh, B. J., Sanchez, J. C., Ou, K., Wilkins, M. R., Tyler, M., ... Hochstrasser, D. F. (1998). '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis, 19(11), 1960-1971. https://doi.org/10.1002/elps.1150191114