Comparison of the intragenomic diversity of 5S rRNA, 16S rRNA gene and 23S rRNA was made, and 5S rRNA has the most widespread intragenomic variation (Fig. 1). The diversity was because of point mutations or single-nucleotide indels; intervening sequences, commonly present in 16S and 23S Rapamycin nmr rRNA genes, were not found in 5S rRNA genes. Twenty-seven genomes with > 10% intragenomic diversity between their 5S rRNA genes were further examined for the impact of the diversity on secondary structure. The two most diversified 5S rRNA genes were selected for the analysis. Secondary
structures of the 5S rRNA genes were constructed based on the principle of minimization of free energy (Mathews et al., 2004), using experimentally defined rRNA as references. In the 27 genomes, there were a total of 421 diversified positions between all pairs of the most dissimilar 5S rRNA genes. Conservative mutations comprised 401 (95.25%) positions, including 125 in loops, 202 covariations, and 74 GU/GC FG 4592 conversions (Table 1). Only 20 (4.75%) of the 421 diversified positions caused changes in the secondary structures of 5S rRNA genes in 14 genomes (Shewanella
amazonensis, Anaerococcus prevotii, Clostridium beijerinckii, Tolumonas auensis, Haemophilus somnus, H. influenzae, A. aphrophilus, S. thermophilum, B. megaterium, P. ingrahamii, L. lactis ssp. cremoris, T. pseudethanolicus, A. pleuropneumoniae, S. saprophyticus ssp. saprophyticus). Only five genomes (C. beijerinckii, T. auensis, H. influenzae, L. lactis ssp. cremoris, and A. pleuropneumoniae) had the secondary structures altered at more than one position in the 5S rRNA genes (Fig. 2). Insertions/deletions Selleck C59 (indels) occurred at 46 of the 421 positions. The 96 genomes with > 3% diversity between 5S rRNA genes (Table S1) can be categorized
into five groups based on the potential mechanisms that may explain the observed high diversity (Fig. 3). (1) Partial operon in which an orphan 5S rRNA gene, unassociated with 16S and 23S rRNA gene, was near an intact rRNA operon (Fig. 3a). In 52 of the 96 genomes with > 3% diversity, the maximal diversity occurred between the orphan 5S rRNA genes and 5S rRNA genes in a complete operon (Table 2), reaching 15.45% in Francisella tularensis ssp. holarctica and 13.04% in Haemophilus ducreyi. (2) Split operon. In 8 of the 96 genomes, the 5S rRNA gene most dissimilar to the majority of other 5S rRNA gene copies was physically separated from the rRNA operon it belongs to (Table 3). For example, in Clostridium perfringens, the 5S rRNA gene rrnH5S (12.61% diversity) was located ~ 240 000-nt from rrnH16S and rrnH23S. Similarly, in Geobacillus kaustophilus, the minor 5S rRNA gene (4.92% diversity) was located ~ 2 800 000-nt from the remaining rRNA operon that contained 16S and 23S rRNA genes. (3) 5S-23S spacer length lineage divergence. In Bacillus, 5S rRNA genes can be grouped based on the 23S-5S spacer length variation.