López-Lara IM, Sohlenkamp C, Geiger O

Language: English
References: 8
Page: 44-45
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Over the last decade, the genomes of several hundreds of organisms have been sequenced (http://www.ncbi.nlm.nih.gov/Genomes/) providing a tremendous amount of data that need to be interpreted and decorated with functions. However, in any newly sequenced bacterial genome, as many as 30-40% of the genes do not have an assigned function.1 This figure is even higher for archaeal and eukaryotic genomes and for the relative large genomes of bacteria with complex life styles, such as rhizobia or Streptomyces. Remarkably, species- or genus-specific genes comprise a relatively small fraction of the uncharacterized genes. The majority of such “hypothetical” genes without any assigned function has a wider phylogenetic distribution and therefore are usually referred to as “conserved hypothetical”. Presently available wholistic approaches such as micro- and macroarrays, protein-protein interaction analyses, etc., can provide important information about regulation and interactions and provide valuable clues for possible functions. However, the majority of genes code for enzymes and presently available whole-scale approaches, such as metabolomics, will reveal new enzymatic functions in a few cases only.

REFERENCES

1. Bork, P. 2000 Powers and pitfalls in sequence analysis: the 70% hurdle. Genome Res. 10:398-400.

2. Gao, J.-L., B. Weissenmayer, A. Taylor, J. Thomas-Oates, I.M. Lopez-Lara & O. Geiger. 2004. Identification of a gene required for the formation of lyso-ornithine lipid, an intermediate in the biosynthesis of ornithine-containing lipids. Mol. Microbiol. 53:1757-1770.

3. Karp, P.D. 2004. Call for an enzyme genomic initiative. Genome Biol. 5:401.

4. López-Lara, I.M., C. Sohlenkamp & O. Geiger. 2003. Membrane lipids in plant-associated bacteria: their biosyntheses and possible functions. Mol. Plant-Microbe Interact. 16: 567-579.

5. Martínez-Morales, F., M. Schobert, I.M. López-Lara & O. Geiger. 2003. Pathways for phosphatidylcholine biosynthesis in bacteria. Microbiology 149:3461-3471.

6. Roberts, R.J., P. Karp, S. Kasif, S. Linn & M.R. Buckley. 2004. A report from the American Academy of Microbiology: An experimental approach to genome annotation. American Society for Microbiology, Washington, D.C.

7. Seffernick, J.L., M.L. de Souza, M.J. Sadowsky & L.P. Wackett. 2001. Melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different. J. Bacteriol. 183:2405-2410.

8. Thomas, J. & J.E. Cronan. 2005. The enigmatic acyl carrier protein phosphodiesterase of Escherichia coli. J. Biol. Chem. 280:34675-34683.