Potential key bases of ribosomal RNA to kingdom-specific spectra of antibiotic susceptibility and the possible archaeal origin of eukaryotes

Abstract

In support of the hypothesis of the endosymbiotic origin of eukaryotes, much evidence has been found to support the idea that some organelles of eukaryotic cells originated from bacterial ancestors. Less attention has been paid to the identity of the host cell, although some biochemical and molecular genetic properties shared by archaea and eukaryotes have been documented. Through comparing 507 taxa of 16S-18S rDNA and 347 taxa of 23S-28S rDNA, we found that archaea and eukaryotes share twenty-six nucleotides signatures in ribosomal DNA. These signatures exist in all living eukaryotic organisms, whether protist, green plant, fungus, or animal. This evidence explicitly supports the archaeal origin of eukaryotes. In the ribosomal RNA, besides A2058 in Escherichia coli vs. G2400 in Saccharomyces cerevisiae, there still exist other twenties of sites, in which the bases are kingdom-specific. Some of these sites concentrate in the peptidyl transferase centre (PTC) of the 23S-28S rRNA. The results suggest potential key sites to explain the kingdom-specific spectra of drug resistance of ribosomes.

Figure 1. Secondary structure of the 18S rRNA of Saccharomyces cerevisiae.

The asterisks in different colours mark the nucleotides specifically shared by different organisms, black: cellular organisms; red: archaea and eukaryotes; and blue: eukaryotes. The bases marked in different colours represent those bases that have been determined to have a specific function: orange: in bridging the small and large subunits, purple: in the A, P and E sites.

Figure 2. Secondary structure of the 25S rRNA of Saccharomyces cerevisiae.

The asterisks in different colours mark the nucleotides specifically shared by different organisms, black: cellular organisms; red: archaea and eukaryotes; and blue: archaea and bacteria. The bases marked in different colours represent those bases that have been determined to have a specific function: orange: in bridging the small and large subunits, purple: in the A, P and E sites; and green: in antibiotic resistance sites in the PTC.

Figure 3. Secondary structure of the 25S rRNA of Saccharomyces cerevisiae.

The asterisks in different colours mark the nucleotides specifically shared by different organisms, black: cellular organisms; red: archaea and eukaryotes; blue: archaea and bacteria; and yellow: bacteria and eukaryotes. The bases marked in different colours represent those bases that have been determined to have a specific function: orange: in bridging the small and large subunits, purple: in the A, P and E sites; and green: in antibiotic resistance sites in the PTC.

Figure 4. The front view of the tertiary structures of the rRNAs of E. coli (A 16S, B 23S) and S. cerevisiae (C 18S, D 25S).

The accession numbers of these structures in the Protein Data Bank are 2I2U, 2I2V, 3O2Z and 3O58, respectively. The pellets in different colours mark the nucleotides specifically shared by different organisms, black: cellular organisms; red: archaea and eukaryotes; blue: archaea and bacteria; and yellow: bacteria and eukaryotes. The functional sites are shown in different colours; orange: in bridging the small and large subunits, purple: in the A, P and E sites, green: in antibiotic resistance sites in the PTC.