Construction of the gyrB Database for the Identification and Classification of Bacteria

Hiroaki Kasai[1] (hkasai@kamaishi.mbio.co.jp)
Kanako Watanabe[1] (kanakow@kamaishi.mbio.co.jp)
Elizabeth Gasteiger[2] (gasteiger@medecine.unige.ch)
Amos Bairoch[2] (bairoch@cmu.unige.ch)
Katsumi Isono[3] (isono@biol.kobe-u.ac.jp)
Satoshi Yamamoto[4] (yamamotost@nichirei.co.jp)
Shigeaki Harayama[1] (harayama@kamaishi.mbio.co.jp)


Abstract

Nucleotide sequences of small-subunit rRNA (16S rRNA) are most commonly used for the identification and characterization of bacteria and their complex communities. However, 16S rRNA evolves slowly and is often not very convenient to resolve bacterial strains at the species level. We have therefore attempted to develop a rapid and more convenient system for bacterial identification using the gyrB gene sequences. We chose the gyrB gene, because (i) it is rarely transmitted horizontally, (ii) its molecular evolution rate is higher than that of 16S rRNA, and (iii) the gene is distributed ubiquitously among bacterial species. We PCR-amplified the 1.2 kb-long gyrB segments from about 1,000 bacterial species by using degenerate primers and determined their nucleotide sequences. The resultant data have been assembled into the gyrB database accessible via WWW.

[ Full-text PDF | Table of Contents ]


Japanese Society for Bioinformatics