Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA

Abstract

The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions and for base covariation revealed that in most eukaryotes the secondary structure of the area consists of 11 helices and includes two pseudoknots. In one of the pseudoknots, exchange of base pairs between the two stems seems to occur, and covariation analysis points to the presence of a base triple. The area also contains three potential insertion points where additional hairpins or branched structures are present in a number of taxa scattered throughout the eukaryotic domain.

Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data

“…Secondary structure information of both rRNAs (Ali et al 1999;Wuyts et al 2000) was used to correct the alignment and to identify expansion segments. The two alignments consisted of 2943 bp (18S rDNA) and 2140 bp (28S rDNA).…”

Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus

“…due to specific deletions typical of this genus. To determine the location of the sites where intragenomic variation of the SSU rRNA gene occurred, the secondary structure of the SSU rRNA molecule was reconstructed based on the models proposed by Wuyts et al (2000Wuyts et al ( , 2001 taking into account the alignment of the sequence with previously reconstructed SSU rRNA models of Amoebozoa (Kudryavtsev 2014;Kudryavtsev et al 2009Kudryavtsev et al , 2014Sims et al 1999). Structure of some of the helices was reconstructed using mfold server (Zuker 2003).…”

“…Numbering of the SSU rRNA structural elements is given hereinafter according to Wuyts et al (2000Wuyts et al ( , 2001. Example of the SSU rRNA secondary structure reconstructed for R. platypodia is shown in Supplementary Fig.…”

“…Analysis of the aligned sequences of revealed 9 areas shared between all 3 species (Supplementary Table S1) demonstrating intragenomic variability located in 8 hypervariable regions of the SSU rRNA gene and in helix 13, which is not assigned to any hypervariable region according to the secondary structure model of SSU rRNA (Wuyts et al 2000(Wuyts et al , 2001. In addition, two 3-nucleotide motifs showing 2 regular substitution patterns each were observed in helices 6/e1 and 23 in R. tribonemae n. sp.…”

Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil

“…Given the fact that the amplified rRNA gene fragment included the most variable regions V3 and V4 (Wuyts et al, 2000), members from a wide range of ciliate groups could be successfully discriminated. Moreover, the comparatively large size of the amplified fragments allowed a reliable taxonomic affiliation of the species by sequencing of the bands.…”