Variations observed in 5S rRNA base compositions are almost entirely due to fixation of point mutations. As a consequence, 5S rRNA size has remained relatively constant during evolution and, therefore, dependencies among the four bases can be predicted. In order to characterize the nature and to determine the degree of such dependencies, correlation analysis followed by principal component factorial analysis was conducted on a large sample of 5S rRNA sequences. The results show that the purine and pyrimidine contents tend to remain constant, so that A + G = Kpur and C + U = Kpyr. The composition of the four bases expressed now by Kpur/Kpyr relationships is also constant (Ks). These relationships imply that the behavior of the mutations in the variable sites of the molecule follows rules imposed by the chemical nature of the bases involved. Consequently, transition mutations would be more favored than substitutions in transversion sites and also than insertion-deletion (rare in 5S rRNAs), since transitions would not significantly alter the values of the Ks-index. A cadeia primária da molécula de RNAr 5S exibe variações na sua seqüência nucleotídica. Tais variações são devidas quase que exclusivamente a fixação de mutações pontuais (transversão e transição). Conseqüentemente, o tamanho da molécula tem permanecido constante e dependências entre as bases são previsíveis. Visando caracterizar a natureza e determinar o grau dessas dependências, procedemos a uma análise de correlação seguida por uma análise fatorial por componente principal da amostragem disponível no Berlin RNA Data Bank. Os resultados demonstram que o conteúdo das purinas e das pirimidinas tende a permanecer constante, de tal forma que A + G = Kpur e C + U = Kpir. Nesses termos, a composição das quatro bases dada agora pela razão Kpur/Kpyr é também igual a uma constante (Ks). O índice Ks implica que o comportamento das mutações nos sítios variáveis da molécula segue regras impostas pela natureza química das bases envolvidas, explicando assim porque as mutações do tipo transição são mais favorecidas na molécula em relação às transversões e às inserções-deleções (raras no 5S), visto que as primeiras não alteram o Ks
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Evolution of metazoan 5S rRNA sequences was analyzed through base composition and types, location and frequency of clustered bases. Characters from sequences of protostomes did not show regular trends as compared with paleontology dating or organism complexity. Trends of increasing G and C, stronger in G clusters, and decreasing A and U, were detected in deuterostomes, in parallel with evolution of complexity. The multifunctional domain 71-104 was highlighted among conserved stretches. Clusters of C were typical of helices. Those of G were longer, extending from helices into loops or related to bulges, which is suggestive of functional significance. Deuterostomian trends were installed early in the lineage and reached full development in aquatic organisms, not increasing further after reptiles. It can be suggested that ribosomal RNA structures participated in deuterostomian high regulatory complexity, either specifically or as part of the widespread processes of chromosomal regionalization.
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