Secondary structure and conserved motifs of the frequently sequenced domains IV and V of the insect mitochondrial large subunit rRNA gene

Abstract

We have analysed over 400 partial insect mitochondrial large subunit (mit LSU) sequences in order to identify conserved motifs and secondary structures for domains IV and V of this gene. Most of the secondary structure elements described by R. R. Gutell et al. (unpublished) for the LSU were identified. However, we present structures for helices 84 and 91 that are not recognized in previous universal models. The portion of the 16S gene containing domains IV and V is frequently sequenced in insect molecular systematic studies so we have many more sequences than previous studies which focused on the complete mitochondrial LSU molecule. In addition, we have the advantage of investigating several sets of closely related taxa. Aligned sequences from thirteen insect orders and nine secondary structure diagrams are presented. These conserved sequence motifs and their associated secondary structure elements can now be used to facilitate the alignment of other insect mit LSU sequences.

Two nearly complete mitogenomes of wheat stem borers, Cephus pygmeus (L.) and Cephus sareptanus Dovnar-Zapolskij (Hymenoptera: Cephidae): An unusual elongation of rrnS gene

“…The deduced structure of H1648 is formed by different helix and loop structures in domain IV including ribosomal binding sites for tRNAs within genus. H2520 is also variable in Cephus mitogenomes like other insects (Buckley et al, 2000;Misof and Fleck, 2003).…”

The phylogeny of the Orthoptera (Insecta) as deduced from mitogenomic gene sequences

“…Similarly, in rrnL, domains I, II, and VI, on average, are less conserved than domains III, IV, and V (Uhlenbusch et al 1987;Gutell et al 1992). So the majority of structural and phylogenetic studies mainly focused on the 3′ half of the rrnL molecule (Kambhampati et al 1996, Flook andRowell 1997a,b;Buckley et al 2000). The 3′ halves of rrnS and rrnL are not very useful for phylogenetic studies of recently diverged species, because they contain few sites that vary (Simon et al 1994).…”

The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera)

“…Compensatory substitutions that would maintain secondary structure are considered to be evidence of actual base pairing (Gutell et al, 1994;Buckley et al, 2000). Unfortunately, very few complete secondary structure models have been proposed for insect mitochondrial rRNA molecules (Misof and Fleck, 2003) and a broader comparative analysis in insects has been performed only on a fragment of the mitochondrial LSU rRNA (Buckley et al, 2000).…”