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Cataloguing life

At my last count, and if you include organelles and viruses, more than 700 complete genomes have been sequenced so far. Bacterial genomes make up the major portion of the organisms sequenced; 32 have been completed and 107 are in progress. Only three eukaryotic genomes, those of Caenorhabditis elegans, Saccharomyces cerevisiae and Drosophila melanogaster have been completed (see the websites: http://www.tigr.org/tdb/mdb/ mdbcomplete. html; http://www.ebi.ac.uk/ genomes/ info.html ). In addition, a draft of the human genome and a large number of human expressed sequence tag (EST) sequences are available and a draft of the mouse genome should be finished shortly. It has become routine to generate catalogues of genes and the next phase of understanding the content of the catalogues is just beginning. Why is the sequencing of the Pseudomonas aeruginosa genome , seemingly just another bacterial genome important? The genus Pseudomonas is not only diverse but is essentially made up of free-living organisms. The majority of bacterial species of which the genomes have been sequenced to date have a parasitic or symbiotic lifestyle, which means that they live in a relatively defined environment. Pseudomonads, by contrast, are just as likely to be found in the soil, the oceans, and in contaminated food as in the lungs and wounds of immunocompromised patients. The striking feature of the P. aeruginosa genome is that its complexity in terms of potential gene products approaches that of the simple eukaryote Saccaromyces cerevisiae. However, comparison of these two genomes based on our current understanding showed very little direct homology between these two organisms. The highest level of similarity that was found by the authors was between P. aeruginosa and Escherischia coli , another well studied gram negative bacterium. Even in this case merely 48% of the genes gave significant matches, with a median amino acid identity of merely 40%. The work published in this paper 1 should lead to a better understanding of the types of functional diversity that are required by a free-living bacterium to survive and successfully compete with other species. P. aeruginosa is also notable for its antibiotic and disinfectant resistance. These abilities are reflected in the complexity of its genome and the products it can generate. Detailed studies of its products will lead to a better understanding of antibiotic resistance in this species and probably in other species as well. The many genome sequencing projects, including the human genome project, are providing a vast amount of information akin to the hieroglyphics on ancient Egyptian tombs. The challenge now facing biological research is to find the Rosetta stone(s) to enable us to decipher the text and translate it into functional relationships between the many individual proteins and sets of proteins that make up a living organism. Comparing the genome databases can yield important clues about the differences between species and act as a guide as we try to fill the many accumulating genetic catalogues with detailed product descriptions.</P> http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Trends in Biotechnology Elsevier
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