Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction

Ribosomal RNAs are important because they catalyze the synthesis of peptides and proteins.Comparative studies of the secondary structure of 18S rRNA have revealed the basic locations of its many length-conserved and lengthvariable regions.In recent years,many more sequences of 18S rDNA with unusual lengths have been documented in GenBank.These data make it possible to recognize the diversity of the secondary and tertiary structures of 18S rRNAs and to identify the length-conserved parts of 18S rDNAs.The longest 18S rDNA sequences of almost every known eukaryotic phylum were included in this study.We illustrated the bioinformatics-based structure to show that,the regions that are more length-variable,regions that are less length-variable,the splicing sites for introns,and the sites of A-minor interactions are mostly distributed in different parts of the 18S rRNA.Additionally,this study revealed that some length-variable regions or insertion positions could be quite close to the functional part of the 18S rRNA of Foraminifera organisms.The tertiary structure as well as the secondary structure of 18S rRNA can be more diverse than what was previously supposed.Besides revealing how this interesting gene evolves,it can help to remove ambiguity from the alignment of eukaryotic 18S rDNAs and to improve the performance of 18S rDNA in phylogenetic reconstruction.Six nucleotides shared by Archaea and Eukaryota but rarely by Bacteria are also reported here for the first time,which might further support the supposed origin of eukaryote from archaeans.

Natural selection on various sites of ribosomal proteins: a cladistic view

Deducing the function of certain sites within a protein necessitates a priori recognition of the strength of selective pressure. Currently, statistical method is the only option to evaluate the degree of conservation. In the statistical framework, the types of selective pressure can be divided into classifications of negative, nearly neutral and positive. However, such quantitative methods may omit some crucial amino acid sites among the nearly neutral results. In this study, we propose that the cladistic information can be also important to evaluate the functional importance of various amino acid sites. The ribosomal proteins of 62 eukaryotic species were chosen as the case for statistical and cladistic analysis. The evolutionary changes of each site in the aligned sequences were matched on a currently well-accepted cladogram of eukaryotes. Hundreds of synapomorphic sites were discovered in various clades, in which only part of them were suggested to be potentially significant in the statistical framework. Notably, the mutation on His213 of RPL10 in human beings, which are synapomorphic in vertebrates but only be identified as being under neutral selection, is account for the disease Autism. Therefore, the cladistic information can be complementary to the statistical framework in understanding lineage-specific selection event. Additionally, the bias in the accumulation of apomorphic amino acids is significant when going from the Chordata to the Mammalia lineages. This study emphasizes the value of analyzing transcriptomic and proteomic data in a cladistic way to recognize the presence of group-specific selection on various sites in proteins.