Group II Intron Structure

Group II introns have a widespread phylogenetic distribution, being found in bacteria and in mitochondrial (mt) and chloroplast (cp) genomes of lower eukaryotes and higher plants. They are relatively common in Gram-negative and Gram-positive bacteria, but rare in archaea. Mobile group II introns that form homing endonucleases range in size from 2-4 kb, and consist of a core catalytic RNA (ribozyme) of 500-1000 nt and an open-reading frame (ORF) of 1.52 kb. Group II intron RNAs have a conserved secondary structure consisting of six domains (DI-DVI), with three major subclasses (IIA, IIB, and IIC) distinguished by specific features (Michel et al. 1989; Michel and Ferat 1995; Toro 2003). This structure is illustrated in Fig. la for the Lactococcus lactis Ll.LtrB intron, an important model system, which belongs to sublcass IIA. DI is the largest domain, and DV is the most highly conserved in sequence. DVI contains the branch-point nucleotide residue, usually a bulged A (Michel et al. 1989). DIV encodes the IEP in a large "loop" and also contains a high-affinity binding site for the IEP in subdomain DIVa (Wank et al. 1999).

In most mobile group II introns, the IEP is a multifunctional protein with RT activity (described in detail below). A few fungal mtDNA group II introns differ in encoding unrelated LAGLIDADG-type DNA homing endonucleases (Toor and Zimmerly 2002), and many mt and cp group II introns do not contain ORFs and are not independently mobile. In Ll.LtrB and other mobile bacterial group II introns, the IEP has its own Shine-Dalgarno (SD) sequence and initiation codon, typically located in or near intron subdomain DIVa (Fig. la; Shearman et al. 1996; Singh et al. 2002). By contrast, in yeast mtDNA coxl-ll and -12 and in many other mt group II introns, the ORF extends upstream from DIV and is translated in frame with the upstream exon, yielding a fusion protein that is processed proteolytically to generate the active IEP (see Fig. 2; Michel and Ferat 1995).

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