Evolution of codon usage and base contents in kinetoplastid protozoans

In this study we analyze and compare the trends in codon usage in fiverepresentative species of kinetoplastid protozoans (Crithidia fasciculata,Leishmania donovani, L. major, Trypanosoma cruzi and T. brucei), with thepurpose of investigating the processes underlying these trends. A principalcomponent analysis shows that the G+C content at the third codon positionrepresents the main source of codon-usage variation, both within species(among genes) and among species. The non- Trypanosoma species exhibitnarrow distributions in codon usage, while both Trypanosoma species presentlarge within-species heterogeneity. The three non-Trypanosoma species havevery similar codon-usage preferences. These codon preferences are alsoshared by the highly expressed genes of T. cruzi and to a lesser degree bythose of T. brucei. This leads to the conclusion that the codon preferencesshared by these species are the ancestral ones in the kinetoplastids. Onthe other hand, the study of noncoding sequences shows that Trypanosomaspecies exhibit mutational biases toward A + T richness, while the non-Trypanosoma species present mutational pressure in the opposite direction.These data taken together allow us to infer the origin of the differentcodon-usage distributions observed in the five species studied. In C.fasciculata and Leishmania, both mutational biases and (translational)selection pull toward G + C richness, resulting in a narrow distribution.In Trypanosoma species the mutational pressure toward A + T richnessproduced a shift in their genomes that differentially affected coding andnoncoding sequences. The effect of these pressures on the third codonposition of genes seems to have been inversely proportional to the level ofgene expression.