Prokaryotic Genomics
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Prokaryotic Genomics B. W. WREN
Introduction Haemophilus influenzae strain Rd became the first free-living organism to have its genome sequenced (Fleischmann et al., 1995). The floodgates have opened with over 100 prokaryotic genomes completely or partially sequenced. However, the acquisition and analysis of sequence data is not an end in itself; instead it is a starting point for generating hypotheses that can be tested in the laboratory. It is clear that knowledge of the complete genome sequence of an organism does not tell us a great deal about the composition or functional capabilities of the organism. Homology, or sequence similarity, provides clues, but it does not prove gene function. Furthermore, a large percentage of genes have no matches to known genes. For example, at the time of sequence release, up to 62% of predicted protein-coding genes in the Methanococcus jannaschii genome had no matches with genes from other organisms (Bult et al., 1996). Elucidating the function of these “ORFan” or “FUN” (function unknown) genes is one of the biggest challenges of the postgenomic era. The avalanche of genome sequence data has coincided with important technological advances in four research areas: bioinformatics, gene mutagenesis, nucleic acid hybridization technology and protein chemistry. These advances will liberate scientific understanding from the piecemeal study of individual genes or operons towards a comprehensive analysis of the entire gene and protein complement of the prokaryotic cell. This new technology will allow a holistic approach to the functional characterization of prokaryotes at the mutational, transcriptional, and protein expression levels (see Fig. 1). The application of functional genomic approaches in the smaller genomes of prokaryotes is the forerunner for the study of functional genomics in higher organisms, including humans. An important exception is the efforts of the Saccharomyces cerevisiae research community, which is a shining example of what can be achieved through functional genomics studies (Lashkari et
al., 1997; Winzeler et al., 1998; Winzeler et al., 1999a; Winzeler et al., 1999b; Uetz et al., 2000).
Prokaryotic Genome Projects and the Birth of Comparative Genomics The availability of genome sequences has spawned the new scientific discipline of comparative genomics, which allows the comparison of genome sequence data between strains, species, genera and even kingdoms. Such studies will provide important taxonomic insights and will have far-reaching implications for the study of evolution. The virtual genome center is a useful webbased site (alces.med.umn.edu/VGC.html) for evolutionary comparisons of proteins, protein families, and genome sequences. In the future, comparative analysis of genome sequence data will be facilitated by high-density array DNA hybridization analysis (see section on Applications of High-Density DNA Arrays and Genomotyping in this Chapter). The salient features of prokaryotic genome sequences are summarized in ch
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