Protein & Cell

, Volume 2, Issue 2, pp 161–170

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

Research Article

DOI: 10.1007/s13238-011-1017-2

Cite this article as:
Xie, Q., Lin, J., Qin, Y. et al. Protein Cell (2011) 2: 161. doi:10.1007/s13238-011-1017-2
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Abstract

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 length-variable 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.

Keywords

secondary structure diversity tertiary structure diversity 18S rRNA Foraminifera Euglenida 

Copyright information

© Higher Education Press and Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  1. 1.Department of Zoology and Developmental Biology, College of Life SciencesNankai UniversityTianjinChina
  2. 2.National Laboratory of Biomacromolecules, Institute of BiophysicsChinese Academy of SciencesBeijingChina
  3. 3.College of Information Technical ScienceNankai UniversityTianjinChina

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