Role of premature stop codons in bacterial evolution

Abstract

When the stop codons TGA, TAA, and TAG are found in the second and third reading frames of a protein-encoding gene, they are considered premature stop codons (PSC). Deinococcus radiodurans disproportionately favored TGA more than the other two triplets as a PSC. The TGA triplet was also found more often in noncoding regions and as a stop codon, though the bias was less pronounced. We investigated this phenomenon in 72 bacterial species with widely differing chromosomal GC contents. Although TGA and TAG were compositionally similar, we found a great variation in use of TGA but a very limited range of use of TAG. The frequency of use of TGA in the gene sequences generally increased with the GC content of the chromosome, while the frequency of use of TAG, like that of TAA, was inversely proportional to the GC content of the chromosome. The patterns of use of TAA, TGA and TAG as real stop codons were less biased and less influenced by the GC content of the chromosome. Bacteria with higher chromosomal GC contents often contained fewer PSC trimers in their genes. Phylogenetically related bacteria often exhibited similar PSC ratios. In addition, metabolically versatile bacteria have significantly fewer PSC trimers in their genes. The bias toward TGA but against TAG as a PSC could not be explained either by the preferential usage of specific codons or by the GC contents of individual chromosomes. We proposed that the quantity and the quality of the PSC in the genome might be important in bacterial evolution.

FIG. 1.

Ternary plot showing the percent distributions of PSC TGA, TAA, and TAG in 72 bacterial genomes. Also shown are their corresponding real stop codons. The forward-tilting dashed grid line (i.e., from left to right) represents a genome's corresponding percentage of TAA. The backward-tilting solid grid line (i.e., from right to left) represents its corresponding percentage of TGA. The horizontal dotted grid line represents the corresponding percentage of TAG. The Rickettsiales are circled as clade A, the Chlamydia/Chlamydophila group is circled as clade B, and the enteric organisms are circled as clade C.

FIG. 2.

Correlation between chromosomal GC content and the percentages of TGA, TAA, and TAG premature stop codon trimers in the genomes of 72 bacterial species. The percentage of TGA in the genomes was positively correlated with the chromosomal GC content, while the percentages of TAA and TAG in the genomes were inversely proportional to the chromosomal GC contents. Lines represents the linear regressions of each data set.

FIG. 3.

Relationships between the average number of PSC per gene in a genome and chromosomal GC content on 72 bacterial genomes. These bacteria are placed according to the ranking of their chromosomal GC contents, from low to high. The insert shows the pairwise comparison of GC content versus PSC per gene and the linear regression line.

FIG. 4.

Correlation between stop codon usages and the GC contents of 72 bacterial chromosomes. TAA as a real stop codon decreases as a function of increasing chromosomal GC content of the organism. TGA as real stop codon increases as a function of increasing GC content of the organism. The use of TAG as real stop codon remains at about 20% regardless to changes in chromosomal GC content. The regression lines are second-order polynomials.