Splicing and evolution of an unusually small group I intron

Abstract

Introns are common in the rRNA gene loci of fungal genomes, but biochemical studies to investigate splicing are rare. Here, self-splicing of a very small (67 nucleotide) group I intron is demonstrated. The PaSSU intron (located within the rRNA small subunit gene of Phialophora americana) splices in vitro under group I intron conditions. Most group I ribozymes contain pairing regions P1-P10, with a conserved G.U pair at the 5' splice site, and a G at the 3' intron border. The PaSSU intron contains only P1, P7, and P10. While it contains the G.U pair at the 5' splice, a U is found at the 3' end of the intron instead of a G. Phylogenetic analysis places it within subgroup IC1, whose members are found in the nuclear rRNA genes of fungi. The structural elements are similar to those in the centermost regions of other group I introns. Its size can be explained by a single large deletion that removed P2 through much of P9. Part of the original P9 region has assumed the function of P7. Its small size and genealogy makes it an excellent model to study RNA catalysis and evolution.

Occurrence and characteristics of group 1 introns found at three different positions within the 28S ribosomal RNA gene of the dematiaceous Phialophora verrucosa: phylogenetic and secondary structural implications

“…An unusually small group 1 intron of 67 bps from the nuclear 18S rDNA has been described in a splicing study of Capronia semiimmersa , a teleomorph of P. americana which is known to be similar to P. verrucosa [20-22]. These small introns contain only P1, P7 and P10 elements, because most of the core regions common in almost all other group 1 introns are missing.…”

Evolution of small putative group I introns in the SSU rRNA gene locus of Phialophora species

“…Previously, the small intron ( Pa SSU) from P. americana Wang 1046 was demonstrated to splice in vivo [14], has group I ribozyme activity in vitro , and phylogenetically falls within the IC1 subgroup [13]. All of the isolates examined (except CDC B3733, which is intron-less) contain small introns (63-75 nt in length, designated Pa SSU, Pv SSU, or Pe SSU) located in the SSU rRNA gene at position 1516 (relative to E. coli ) that can form similar secondary structures (Figure 2).…”

“…Triangles indicate clades that are summarized for simplicity, as indicated as follows: Clade A, subgroup IC1 introns from Ascolacicola austriaca, Cryptendoxyla hypophloia , and Leucostoma personii ; Clade B, subgroup IC1 introns from Gaeumannomyces graminis , Hypocrea pallida , Mycoarachis inversa , and Nectria aureofulva ; Clade C, subgroup IC1 introns from Apioplagiostoma aceriferum , Cephalotheca sulfurea , Cordycepioideus bisporus , and Gnomoniella tubiformis; Clade D, subgroup IC1 introns from Ahtiana sphaerosporella , Arctocetraria nigricascens , Arctoparmelia centrifuga , Asahinea chrysantha , Cavernularia lophyrea , Cetraria ericetorum , Cetraria islandica (3 isolates), Cetraria nigricans , Cladonia arbuscula , Melanelia hepatizon , Melanelixia fulginosa , Myelochroa metarevuluta , Nephromopsis ahtii , Nephromopsis komarovii , Nephromopsis laureri , Nephromopsis stracheyi , Parmelia cochleata , Parmelia fertilis , Parmelia saxatilis , Parmelia squarrosa , Parmelia sulfata , Pseudophebe pubescens , Tuckermanella coralligera , Tuckermanella orbata , Tuckermanella playyphylla , Vulcipida pinasrti and Vulcipida viridis . Accession numbers for the Phialophora sequences are provided in Table 1, while those for the other sequences are listed in reference [13]. Lengths of the introns are indicated within the parentheses, as are the physical positions in the rRNA genes.…”

“…In previous studies we reported the presence of self-splicing group I introns in the rRNA small subunit (SSU) genes of Cenococcum geophilum [12], as well as the location and self-splicing ability of a small (67 nucleotides, nt) group I intron in Phialophora americana Wang 1046 [13,14]. This small intron may have originated from an unequal crossover in an ancestor that was amplified in the genome.…”

Identification of group I introns within the SSU rDNA gene in species of Ceratocystiopsis and related taxa

“…Nuclear rDNA group I introns range in size from 250 to 600 nucleotides (nt), although there are examples that exceed 1000 nt (Haugen et al 2004). There are also highly compact group I introns at 62e78 nt and these introns appear to be IC1 introns that only maintained the P1, P7, and P10 paired regions, however they still have self-splicing capacity (Harris & Rogers 2008).…”