|Meinersmann, Richard - Rick|
Submitted to: Genome Letters
Publication Type: Peer reviewed journal
Publication Acceptance Date: 10/10/2003
Publication Date: 12/1/2003
Citation: Wassenaar, T.M., Meinersmann, R.J. 2003. The tga stop codon and the phylogeny of the selenocysteine pathway. Genome Letters. 2(4):127-138. Interpretive Summary: The DNA sequences of the genomes for several bacteria are now known. Most bacteria that are associated with foodborne illness have a biochemical pathway, the formate dehydrogenase pathway, that requires using the genetic code in a non-standard way for the use of an unusual amino acid in the protein, selenocysteine. This in turn requires an additional set of genes for making selenocysteine and inserting it into the protein. Thus the pathway is costly to the organism and costly pathways tend to be important. This study was design to see if the distribution and evolution of this pathway gives clues to the costs. The genetic code that is critical for selenocysteine use is TGA. We found that TGA is used in special context that is not directly related to the use of selenocysteine. We also found that the evolution of the selenocysteine usage indicates that it was an ancient trait that was probably common to all bacteria at one time and was lost by many modern species. That means that the system is disposable for life but must be retained by other species because of the advantage that it gives. That is to say, the cost is worth the advantage. Therefore, this pathway could be a high priority for intervening in the life cycle of foodborne pathogens.
Technical Abstract: The genomes of 5 Archaea and 21 Eubacteria representing 26 genera were studied for their stop codon usage and the presence of the machinery to incorporate selenocysteine. Members of 9 genera, including most of the gamma subdivision of the Proteobacteria, have been annotated, or were found to have, the genes selABD, machinery needed for incorporation of selenocysteine for the UGA codon. A stem-loop structure immediately following the UGA is needed for selenocysteine incorporation in Escherichia coli formate dehydrogenase. Seven of the bacterial genomes had homologues of the formate dehydrogenase with the TGA codon at the same site. However, stem-loop structures were much weaker following those TGA codons in the formate dehydrogenase homologues than seen with E. coli. We examined the context of the different stop codons that were used in all annotated ORFs for clues on the regulation of selenocysteine incorporation. It was found that genes ending in TGA were likely in almost all bacteria to overlap with the downstream gene by 4 bases. This was extreme in Campylobacter jejuni, which has selABD and formate dehydrogenase containing TGA within the reading frame. Of all genes ending in TGA in C. jejuni (25.5% of all genes), 60% of genes had the 4 base overlap. In Pseudomonas aeruginosa, which also has the selenocysteine pathway, 78% of stop codons were found to be TGA of which 11.9% overlapped by 4 bases with the downstream gene. The phylogeny of SelABD and formate dehydrogenase suggests that the system was anciently acquired and lost by many modern bacteria. The context of the use of TGA may be a remnant of a regulatory mechanism for the incorporation of selenocysteine