Figure 1.
Conservation of 2° structure by complex rearrangement of base pairing and substitutions in rrn23S of Nocardia farcinica (A and B) and Clostridium perfringens (C and D).
Nucleotides related to substitutions are highlighted in red and indels in green. Segments of rrn23S of Nocardia farcinica shown correspond to positions 620 through 659 of rrnC23S. The segments of rrnC23S (A) and rrnB23S (B) differ by 9 positions, including one indel and eight substitutions. Segments of rrn23S of Clostridium perfringens shown correspond to positions 292 through 406 of rrnH23S. The segments of rrnH23S (C) and rrnD23S (D) differ by 22 positions, including 13 indels and 8 substitutions.
Table 1.
Genomes with significant intragenomic diversity among paralogous 23S rRNA genes.
Figure 2.
Distribution of substituted positions and IVS in 23S rRNA genes of T. tengcongensis.
Secondary structure of rrnB16S and rrnB23S was based on the 2° structure models for Thermus thermophilus [14]. Substituted positions between rrnB23S and rrnC23S are highlighted in colors according to the position-specific relative variability rate calculated from the consensus rrn23S model based on an alignment of 184 bacterial 23S rRNA genes [14]. A position with a relative substitution rate v>1 (red) implies that it has a substitution rate higher than the average substitution rate of all its sites in the rRNA gene analyzed, while v<1 (blue) indicates that the rate is lower than the average rate. Uncommon sites are positions that are occupied in <25% of organisms because of insertions, which are shown by black dots.
Table 2.
Observed and expected variability in 23S rRNA genes in T. tengcongensis.
Table 3.
Genomes with intervening sequences in 23S rRNA genes.
Figure 3.
IVS in Nostoc sp (strain PCC 7120) 23S rRNA genes.
A 1471-bp IVS flanked by partial 16-bp inverted repeats (arrows) was found in rrnA23S, which contains a 963-bp open reading frame that encodes proteins with strong homology (Expected value = 7e−27) to transposases 9 and 20 in COG3547.
Figure 4.
IVS in Deinococcus radiodurans 23S rRNA genes.
rrnA23S contains a 1067-bp IVS flanked by 27-bp inverted repeats. The arrows indicate the location of the inverted repeats. The 1067-bp insert contains a 516-bp open reading frame encoding a 172-amino acid protein with strong homology (Expected value = 8e−14) to predicted transposase COG3335.