Genomic Analysis of the Genes Encoding Ribosomal Proteins in Eight Eubacterial Species and Saccharomyces cerevisiae

Katsutoshi Fujita[1] (fujita@biol.kobe-u.ac.jp)
Tomoya Baba[2] (baba@staff.or.jp)
Katsumi Isono[1] (isono@biol.kobe-u.ac.jp)

[1] Graduate School of Science and Technology, Kobe University
Rokkodai, Kobe 657-8501, Japan
[2] STAFF, Kamiyokoba, Ippaizuka, Tsukuba 305-0854, Japan


Abstract

The complete genomic nucleotide sequence data of more than 10 unicellular organisms have become available. During the past years, we have been focusing our attention to the analysis of the structure and function of the ribosome and its protein components. By making use of the genomic sequence data, our work can now be extended to comparative analysis of the ribosomal components at the genomic level. Such analysis will contribute to our understanding of the structure-function relationship of the ribosome that is vital to the expression of genetic information. Bearing these in mind, the ribosomal protein genes of organisms whose genomic sequence data are available were analyzed, which included Aquifex aeolicus; Archaeoglobus fulgidus; Borrelia burgdorferi; Bacillus subtilis; Escherichia coli; Haemophilus influenzae; Helicobacter pylori; Methanococcus jannaschii; Mycoplasma genitalium; Mycoplasma pneumoniae; Synechosystis sp., and Saccharomyces cerevisiae. In addition, the amino acid sequence data of Bacillus stearothermophilus ribosomal proteins were used in the evolutionary evaluation. The results indicate that, in eubacteria including two species of Mycoplasma, the operon structure of ribosomal protein genes is well conserved, while their relative orientation and chromosomal location are diverged into several classes. The operon structure in M. jannaschii on the other hand is quite different from the eubacterial one and we noticed that its many genes show similarity to rat ribosomal protein genes. The degrees of sequence conservation differ from one ribosomal protein gene to another, but several genes encoding proteins that are considered to be of structural importance are conserved throughout the bacterial species including archaebacteria and further in S. cerevisiae.

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Japanese Society for Bioinformatics