Figure 1.
Secondary structure of human 5S rRNA.
In all organisms, the structure consists of five double-stranded regions (I–V) and five loops (A–E). Loop E, which differs between eukaryotic and eubacterial 5S rRNAs, is highlighted in yellow.
Figure 2.
The phylogenetic tree constructed by the concatenated sequences of SSU and LSU rRNA based on GTR+G model.
Numbers indicate the bootstrap scores for ML (left) and Bayesian posterior probabilities for Bayesian (right) that supported the indicated node. Taxon names are color coded according to the taxonomic order designation at NCBI. (A)Animal. Green: chordata, blue: arthropoda, red: nematoda, black: outgroup. (B) γ-proteobacteria. Green: virionales, blue: enterobacteriales, red: alteromonadales, violet: pseudomonadales, black: outgroup.
Figure 3.
The accuracy of ancestral states reconstruction.
Frequencies of marginal posterior probabilities calculated for the most likely nucleotide reconstruction at each site of the ancestral 5S rRNA sequence under the GTR+G model.
Table 1.
Coevolving positions detected in eukaryotic and eubacterial 5S rRNA.
Figure 4.
An example of coevolving pairs 8-111 detected in animal 5S rRNA sequences.
The disruption of GC pair was compensated by a G8A substitution that created an AU pair or by a U111C substitution that restored the GC pair. Intermediate states are shown in blue.
Table 2.
Number of compensatory switches in 5S rRNAs.
Figure 5.
Evolutionary secondary structure maps of 5S rRNA.
(A) Cenancestor 5S rRNA structure. (B) Human 5S rRNA secondary structure. Compensatory substitutions that restored Watson-Crick pairs were shown in yellow. Coevolutionary interactions of multiple stem pairs were shown in violet and interactions of stem and loop structures were shown in green.
Table 3.
Observed and Expected Substitutions in 5S rRNAs.
Figure 6.
Compensatory substitutions that maintain base pairing contribute significantly to the stabilization of RNA structure.
(A) Changes in unpaired bases within stems during the evolution of 5S rRNA. (B) Evolutionary secondary structure from ancestor to human 5S rRNA. (C) Changes in paired bases within stems of native and simulated 5S rRNA sequences.
Table 4.
Stability of animal 5S rRNA secondary structures.
Figure 7.
Overall rates of evolution for different stem regions.