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Journal of Bacteriology, October 2008, p. 6718-6725, Vol. 190, No. 20
0021-9193/08/$08.00+0     doi:10.1128/JB.00682-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Role of Premature Stop Codons in Bacterial Evolution{triangledown}

Tit-Yee Wong,1* Sanjit Fernandes,1 Naby Sankhon,1 Patrick P. Leong,2 Jimmy Kuo,3 and Jong-Kang Liu4

Department of Biology, Bioinformatics Program, The University of Memphis, Memphis, Tennessee,1 Gigamon Systems, Milpitas, California,2 Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan, Republic of China,3 Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan, Republic of China4

Received 14 May 2008/ Accepted 4 August 2008

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.

* Corresponding author. Mailing address: LS 523, Biology Department, The University of Memphis, Memphis, TN 38152. Phone: (901) 678-4462. Fax: (901) 678-4457. E-mail: tywong{at}memphis.edu

{triangledown} Published ahead of print on 15 August 2008.

Journal of Bacteriology, October 2008, p. 6718-6725, Vol. 190, No. 20
0021-9193/08/$08.00+0     doi:10.1128/JB.00682-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.





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