DNA sequence sampling of the Streptococcus pneumoniae genome to identify novel targets for antibiotic development

We initiated a survey of the Streptococcus pneumoniae genome by DNA sequenc e sampling. More than 9,500 random DNA sequences of approximately 500 bases average length were determined. Partial sequences sufficient to identify a pproximately 95% of the aminoacyl tRNA synthetase genes and ribosomal prote in (rps) genes were found by comparing the database of partial sequences to known sequences from other organisms. Many genes involved in DNA replicati on, repair, and mutagenesis are present in S, pneumoniae, Genes for the maj or subunits of RNA polymerase are also present, as are genes for two altern ative sigma factors, rpoD and rpoN, Many genes necessary for amino acid or cofactor biosynthesis and aerobic energy metabolism in other bacteria appea r to be absent from the S, pneumoniae genome. A number of genes involved in cell wall biosynthesis and septation were identified, including six homolo gs to different penicillin binding proteins. Interestingly, four genes invo lved in the addition of D-alanine to lipoteicoic acid in other gram positiv e bacteria were found, even though the lipoteicoic acid in S, pneumoniae ha s not been shown to contain D-alanine, The S, pneumoniae genome contains a number of chaperonin genes similar to those found in other bacteria, but ap parently does not contain genes involved in the type In secretion commonly observed in gram negative pathogens. The G+C content of S, pneumoniae genom ic DNA is approximately 43 mole percent and the size of the genome is appro ximately 2.0 Mb as determined by pulsed-field gel electrophoresis, Many of the genes identified by sequence sampling have been physically mapped to th e 19 different SmaI fragments derived from the S, pneumoniae genome. The da tabase of random genome sequence tags (GSTs) provides the starting material for determining the complete genome sequence, gene disruption analysis, an d comparative genomics to identify novel targets for antibiotic development .