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Group II introns are a large class of self-catalytic ribozymes and mobile genetic elements found within the genes of all three domains of life. Ribozyme activity (e.g., self-splicing) can occur under high-salt conditions in vitro. However, assistance from proteins is required for in vivo splicing. In contrast to group I introns, intron excision occurs in the absence of GTP and involves the formation of a lariat, with an A-residue branchpoint strongly resembling that found in lariats formed during splicing of nuclear pre-mRNA. It is hypothesized that pre-mRNA splicing (see spliceosome) may have evolved from group II introns, due to the similar catalytic mechanism as well as the structural similarity of the Domain V substructure to the U6/U2 extended snRNA. Finally, their ability to site-specifically mobilize to new DNA sites has been exploited as a tool for biotechnology.
Structure and catalytic site
The secondary structure of group II introns is characterized by six typical stem-loop structures, also called domains I to VI or D1 to D6. The domains radiate from a central core that brings the 5' and 3' splice junctions into close proximity. The proximal helix structures of the six domains are connected by a few nucleotides in the central region (linker or joiner sequences). Due to its enormous size, the domain 1 was divided further into subdomains a, b, c, and d. Sequence differences of group II introns that led to a further division into subgroups IIA and IIB were identified. Group II introns also form very complicated RNA Tertiary Structure.
Group II introns possess only a very few conserved nucleotides, and the nucleotides important for the catalytic function are spread over the complete intron structure. The few strictly conserved primary sequences are the consensus at the 5' and 3' splicing site (...↓GUGYG&... and ...AY↓...), some of the nucleotides of the central core (joiner sequences), a relatively high number of nucleotides of D5 and some short-sequence stretches of D1. The unpaired adenosine in D6 (marked by an asterisk in the figure and located 7 or 8 nt away from the 3' splicing site) is also conserved and plays a central role in the splicing process.
In 2005, A. De Lencastre et al. found that during splicing of Group II introns, all reactants are preorganized before the initiation of splicing. The branch site, both exons, the catalytically essential regions of D5 and J2/3, and epsilon−epsilon' are in close proximity before the first step of splicing occurs. In addition to the bulge and AGC triad regions of D5, the J2/3 linker region, the epsilon−epsilon' nucleotides and the coordination loop in D1 are crucial for the architecture and function of the active-site.
Group II catalytic intron
Group II catalytic introns are found in rRNA, tRNA, and mRNA of organelles (chloroplasts and mitochondria) in fungi, plants, and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). This model and alignment represents only domains V and VI. A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can, therefore, be up to 3 kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long-range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB, which differ in splice site consensus, and the distance of the bulged adenosine in domain VI (the prospective branch point forming the lariat) from the 3' splice site.
- Seetharaman, M; Eldho, NV; Padgett, RA; Dayie, KT (Feb 2006). "Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA". RNA. 12 (2): 235–47. doi:10.1261/rna.2237806. PMC . PMID 16428604.
- Valadkhan, S (May–Jun 2010). "Role of the snRNAs in spliceosomal active site". RNA biology. 7 (3): 345–53. doi:10.4161/rna.7.3.12089. PMID 20458185.
- de Lencastre A, Hamill S, Pyle AM (July 2005). "A single active-site region for a group II intron". Nat. Struct. Mol. Biol. 12 (7): 626–7. doi:10.1038/nsmb957. PMID 15980867.
- Bonen, L; Vogel J (2001). "The ins and outs of group II introns". Trends Genet. 17 (6): 322–331. doi:10.1016/S0168-9525(01)02324-1. PMID 11377794.
- Chu, VT; Adamidi C; Liu Q; Perlman PS; Pyle AM (2001). "Control of branch-site choice by a group II intron". EMBO J. 20 (23): 6866–6876. doi:10.1093/emboj/20.23.6866. PMC . PMID 11726522.
- Lehmann, K; Schmidt U (2003). "Group II introns: structure and catalytic versatility of large natural ribozymes". Crit Rev Biochem Mol Biol. 38 (3): 249–303. doi:10.1080/713609236. PMID 12870716.
- Michel F, Umesono K, Ozeki H (October 1989). "Comparative and functional anatomy of group II catalytic introns--a review". Gene. 82 (1): 5–30. doi:10.1016/0378-1119(89)90026-7. PMID 2684776.
You can either download the motif alignment or view it directly in your browser window. More...
You can download (or view in your browser) a text representation of a Rfam alignment in various formats:
- Gapped FASTA
- Ungapped FASTA
You can view or download motif alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".
There are 18 Rfam families which match this motif.
This section shows the families which have been annotated with this motif. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...
To annotate the family with a motif model, the seed sequence was first filtered using a 0.9 fraction identity cut-off. The filtered seed was then scanned using Infernal cmscan (v1.1) with a concatenated CM file containing each of the motifs. Significance of hits between a seed sequence and the CM was based on a gathering threshold that was individually set for each motif. Only motifs where more than two and at least 10% of seed sequences scored higher than the gathering threshold were included for the next stage of processing. These subsets of motifs were then rescanned against the entire (non-filtered) seed to generate matches.
Number of Hits: the number of sequences in the family seed that score above the gathering threshold from motif.
Fraction of Hits: the fraction of sequences in the family seed that score above the gathering threshold from motif.
Sum of Bits: the sum of the bit scores of matches between the motif and the family seed sequence.
Image: plot illustrating where on the consensus secondary structure matches occur between seed sequences and the motif model.
|Original order||Family Accession||Family Description||Number of Hits||Fraction of Hits||Sum of Bits||Image|
|3||RF00011||Bacterial RNase P class B||16||0.140||174.9|
|3||RF00018||CsrB/RsmB RNA family||19||0.500||202.5|
|3||RF00026||U6 spliceosomal RNA||172||0.915||3759.8|
|3||RF00029||Group II catalytic intron||92||1.000||3204.8|
|3||RF00300||Small nucleolar RNA Z221/R21b||2||0.167||22.1|
|3||RF00413||Small nucleolar RNA SNORA19||2||0.059||27.6|
|3||RF00449||HIF-1 alpha IRES||6||0.353||73.6|
|3||RF00553||Small Cajal body specific RNA 1||4||0.138||44.2|
|3||RF01071||Ornate Large Extremophilic RNA||2||0.100||27.8|
|3||RF02356||Alphaproteobacterial sRNA BjrC1505||2||0.080||22.3|
|3||RF02384||FasX small RNA||2||0.250||20.4|
|3||RF02540||Archaeal large subunit ribosomal RNA||16||0.176||236.7|
|3||RF02541||Bacterial large subunit ribosomal RNA||21||0.206||258.2|
|3||RF02542||Microsporidia small subunit ribosomal RNA||6||0.130||64.8|
|3||RF02543||Eukaryotic large subunit ribosomal RNA||23||0.261||295.7|
This section shows the database cross-references that we have for this Rfam motif.
Seetharaman M, Eldho NV, Padgett RA, Dayie KT RNA. 2006;12:235-47. Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA. PUBMED:16428604
Valadkhan S RNA Biol. ;7:345-53. Role of the snRNAs in spliceosomal active site. PUBMED:20458185
External database links
Curation and motif details
This section shows the detailed information about the Rfam motif. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.
cmbuild -F CM SEED
|Covariance model||Download the Infernal CM for the motif here|