ARS | Publication request: 9TH INTERNATIONAL CONFERENCE ON MICROBIAL GENOMES

Submitted to: International Conference on Microbial Genomes
Publication Type: Abstract Only
Publication Acceptance Date: September 15, 2001
Publication Date: September 29, 2001
Citation: MEINERSMANN, R.J., WASSENAAR, T. 9TH INTERNATIONAL CONFERENCE ON MICROBIAL GENOMES. INTERNATIONAL CONFERENCE ON MICROBIAL GENOMES. 2001.

Technical Abstract: The genomes of 7 Archaea and 21 Eubacteria representing 28 genera were studied for their stop codon usage. Members of 7 genera, including most of the gamma subdivision of the Proteobacteria, have been documented to have the genes selABD and SeCys-tRNA, 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. However, such a stem-loop structure is missing from the formate dehydrogenase homologue found in Campylobacter jejuni, an epsilon subdivision Proteobacteria that also has the genes needed for selenocysteine incorporation. We examined the context that the different stop codons were used for clues on the regulation of selenocysteine incorporation. It was found that genes ending in TGA were very likely in almost all bacteria to overlap with the downstream gene by 4 bases. This was extreme in C. jejuni, 60% of genes ending in TGA had the 4 base overlap. Genes ending in TAA or TAG were similar to each other in their positional relation to the downstream gene with a mode of between 10 to 20 bases. It was also found that genes predicted to be highly expressed are less likely to follow a gene that ends in TGA. 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.