Secondary Structure and Molecular Evolution of the Mitochondrial Small Subunit Ribosomal RNA in Agaricales (Euagarics clade, Homobasidiomycota)

Abstract

The complete sequences and secondary structures of the mitochondrial small subunit (SSU) ribosomal RNAs of both mostly cultivated mushrooms Agaricus bisporus (1930 nt) and Lentinula edodes (2164 nt) were achieved. These secondary structures and that of Schizophyllum commune (1872 nt) were compared to that previously established for Agrocybe aegerita. The four structures are near the model established for Archae, Bacteria, plastids, and mitochondria; particularly the helices 23 and 37, described as specific to bacteria, are present. Within the four Agaricales (Homobasidiomycota), the SSU-rRNA "core" is conserved in size (966 to 1009 nt) with the exception of an unusual extension of 40 nt in the H17 helix of S. commune. The four core sequences possess 76% of conserved positions and a cluster of C in their 3' end, which could constitute a signal involved in the RNA maturation process. Among the nine putative variable domains, three (V3, V5, V7) do not show significant length variations and possess similar percentages of conserved positions (69%) than the core. The other six variable domains show important length variations, due to independent large size inserted/deleted sequences, and higher rates of nucleotide substitutions than the core (only 31% of conserved positions between the four species). Interestingly, the inserted/deleted sequences are located in few preferential sites (hot spots for insertion/deletion) where they seem to arise or disappear haphazardly during evolution. These sites are located on the surface of the tertiary structure of the 30S ribosomal subunit, at the beginning of hairpin loops; the insertions lead to a lengthening of existing hairpins or to branching loops bearing up to five additional helices.

Massively Convergent Evolution for Ribosomal Protein Gene Content in Plastid and Mitochondrial Genomes

“…On the one hand, identification of genes encoding r-proteins is complicated from biased fungal mitochondrial genomes as seen in the case of rps 3 (Bullerwell et al 2000); on the other hand, fungal mitochondrial genomes vary in the lengths of their rRNAs. However, at least in some studied cases, fungal SSU rRNAs share a conserved rRNA core region approximately equal in length to animal mitochondrial SSU rRNAs, and additional sequences, which inflate rRNA lengths, might be inserted into hotspots for insertions/deletions and map to the surface of the 30S ribosome (Barroso et al 2003). This currently precludes a clear statement on the correlation between rRNA length and presence/absence of r-proteins in fungal mitochondria.…”

Phylogeny, taxonomy, and character evolution inEntolomasubgenusNolanea

“…The mtSSU was the second last performing marker and had the second highest scale factor. The mtSSU evolves mainly in its variable domains, including large insertions and deletions which are sometimes difficult to align accurately ( Barroso et al 2003 , Hong & Jung 2004 ). The evolutionary rate can thus be underestimated when unique sequence fragments are excluded from the analysis due to the lack of alignable counterparts ( Bruns & Szaro 1992 ).…”

“…The positions of the variable domains V1–V6 were inferred from the detailed annotations of the sequence of L . edodes given by Barroso et al (2003) . The primers and variable domains were mapped on the mtSSU sequence of T. matsutake ( Fig.…”