A possible tertiary rRNA interaction between expansion segments ES3 and ES6 in eukaryotic 40S ribosomal subunits

Abstract

Eukaryotic 16S-like ribosomal RNAs contain 12 so-called expansion segments, i.e., sequences not included in the RNA secondary structure core common to eubacteria, archaea, and eukarya. Two of these expansion segments, ES3 and ES6, are juxtaposed in the recent three-dimensional model of the eukaryotic 40S ribosomal subunit. We have analyzed ES3 and ES6 sequences from more than 2900 discrete eukaryotic species, for possible sequence complementarity between the two expansion segments. The data show that ES3 and ES6 could interact by forming a helix consisting of seven to nine contiguous base pairs in almost all analyzed species. We, therefore, suggest that ES3 and ES6 form a direct RNA-RNA contact in the ribosome.

FIGURE 1.

Secondary structure model of 18S rRNA (Gutell 1993) showing the position of expansion sequences ES3 (red) and ES6 (blue) (Gerbi 1996). The sequences of the proposed complementary regions in ES3 and ES6 are shown for wheat Triticum aestivum and mouse Mus musculus, GenBank accession nos. AY049040 and X00686, respectively. (Inset) Position of ES3 (red) and ES6 (blue) in the 40S ribosomal subunit (Spahn et al. 2001). The 40S subunit is shown from the inter-subunit side (left) and from the solvent side (right).

FIGURE 2.

Base composition and maximum length of the complementary sequences in ES3 and ES6 from different taxa. Sequence information for >2900 discrete species was taken from the European Small Subunit Ribosomal Database (http://rrna.uia.ac.be/ssu/index.html; Wuyts et al. 2002). (ES 3, ES 6) The relative abundance (%) of each of the four bases at the nine positions in the two putative complementary sequences (ES3 and ES6). (Base pairs) The maximum possible number of continuous base pairs formed by the complementary sequences in ES3 and ES6. The bars represent the percentage of species within each group that could form a complementary helix of indicated length. The number of species in each taxon or group of organisms within a taxon is given in parentheses. The taxa listed correspond to the taxonomy usage given by the National Institute for Biotechnology Information (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html).