General Trends in Selectively Driven Codon Usage Biases in the Domain Archaea

Journal of Molecular Evolution - Tập 79 - Trang 105-110 - 2014
Andrés Iriarte1,2,3, Eugenio Jara1, Lucía Leytón1, Leticia Diana1,4, Héctor Musto1
1Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias, UdelaR, Montevideo, Uruguay
2Dpto. de Bioquímica y Genómica Microbianas and Dpto. de Genómica, IIBCE, Montevideo, Uruguay
3Dpto. de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, UdelaR, Montevideo, Uruguay
4Area Bacteriología, Dpto. de Microbiología, Facultad de Veterinaria, UdelaR, Montevideo, Uruguay

Tóm tắt

Since the advent of rapid techniques for sequencing DNA in the mid 70’s, it became clear that all codons coding for the same amino acid are not used according to neutral expectations. In the last 30 years, several theories were proposed for explaining this fact. However, the most important concepts were the result of analyses carried out in Bacteria, and unicellular and multicellular eukaryotes like mammals (in other words, in two of the three Domains of life). In this communication, we study the main forces that shape codon usage in Archaeae under an evolutionary perspective. This is important because, as known, the orthologous genes related with the informational system in this Domain (replication, transcription and translation) are more similar to eukaryotes than to Bacteria. Our results show that the effect of selection acting at the level of translation is present in the Domain but mainly restricted to only a phylum (Euryarchaeota) and therefore is not as extended as in Bacteria. Besides, we describe the phylogenetic distribution of translational optimal codons and estimate the effect of selection acting at the level of accuracy. Finally, we discuss these results under some peculiarities that characterize this Domain.

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