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In the leptosporangiate fern Osmunda regalis, cox1 gene is disrupted by a 1071-nucleotide-long group I intron that is homologous to the Marchantia polymorpha cox1 intron 4 (cox1i395g1). This intron, which shares 89% sequence identity with its bryophyte counterpart, lost the capacity to encode for a maturase due to insertion/deletion mutations. The cox1 coding region is interrupted by a stop codon in both exons. The cox1 transcript undergoes 58 C-to-U and 13 U-to-C conversions, including the suppression of two stop codons that result in the recovery of a functional cox1 ORF. Interestingly, 4 C-to-U conversions found in mRNA precursors showed that the O. regalis cox1i395g1 intron is efficiently edited. These modifications improved the sequence identity with the Marchantia cox1i395 intron. In particular, the RNA editing events affect regions involved in secondary and tertiary structures of the intron, restoring three base pairing in the structural P5a and P9 helices, and correcting a highly conserved U in the P7 helix that contributes to the catalytic core. Moreover, cox1 intron orthologous from three different fern species were found to be edited by both C-to-U and U-to-C conversions in P7 and P9. Thus, RNA editing helps to correct the conserved domains of group I introns in 'true ferns', suggesting a possible link between editing and splicing. We present here the first experimental evidence of RNA editing concerning a group I intron in plant organelles. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Intron origin and evolution are of high interest, yet the rates of insertion and loss are unclear. To investigate their spread, we studied ribosomal (r)DNA introns from the closely related lichens Physcia aipolia and P. stellaris. Both taxa are replete with rDNA spliceosomal introns and autocatalytic group I introns, many of which show presence/absence polymorphism when screened with the PCR approach. This initially suggested that Physcia could be a model for studying intron retention and loss. However, during the course of a population-level analysis, we discovered widespread intron presence/absence heterogeneity within lichen thalli. To address this result, we sequenced multiple clones encoding nuclear rDNA and the single-copy elongation factor-1α ( EF-1α) from individual thalli. These data showed extensive rDNA heterogeneity within individuals, rather than the presence of multiple fungi within a thallus. Our results suggest that considerable care must be taken when interpreting intron presence/absence in lichen rDNA, an observation that has general implications for the study of rDNA intron evolution. [ABSTRACT FROM AUTHOR]

A phylogenetic investigation of the autosporic chlorophycean alga speciesSelenastrum capricornutumusing the small subunit (SSU) rRNA gene revealed the unusual presence of six group IC1 introns. Previous studies showed that numerous green algal taxa contain group IC1 introns. However, whereas some algal species harbor multiple introns in a single ribosomal gene, none have contained as many asS. capricornutum. Three of theS. capricornutumintrons are located at conserved algal intron sites and the remaining three are located at novel eukaryotic positions. The SSU rRNA genes and their introns have been sequenced and putative secondary structures are proposed for the introns. Also, their similarity to other group IC1 introns from algal, fungal, and viral sources is investigated. Results suggest the initial presence of introns at conserved locations, followed by duplication and insertion to novel positions within the SSU rRNA gene. [ABSTRACT FROM AUTHOR]

The protein encoded by the second intron (bi2) of the mitochondrial cyt b gene from Saccharomyces cerevisiae functions as a maturase promoting intron splicing. This protein belongs to a large family characterized by the presence of two conserved motifsauthor="alan" time="20040513T082332+0000":author="alan" time="20040513T082334+0000" data=";" LAGLIDADG (or P1 and P2). We have isolated and characterized spontaneous revertants from two mis-sense mutations, G85D and H92Pauthor="alan" time="20040513T082434+0000" data=","author="alan" time="20040513T082437+0000" (localized in the P1 motif of the bi2author="alan" time="20040513T083211+0000"-author="alan" time="20040513T082359+0000" data="-"maturaseauthor="alan" time="20040513T082439+0000"), that have a detrimental effect on intron splicing. All analyzed revertants are intragenic and resulted from monosubstitutions in the mutated codons. Only true backauthor="alan" time="20040513T082508+0000"-author="alan" time="20040513T082508+0000" data=" "mutations author="alan" time="20040513T082526+0000"that restorauthor="alan" time="20040513T082528+0000"eauthor="alan" time="20040513T082529+0000" data="ing" the initial glycineauthor="alan" time="20040513T082515+0000" author="alan" time="20040513T082512+0000" data=" "85 and a pseudoreversion that replaces the deleterious aspartic acidauthor="alan" time="20040513T082531+0000" author="alan" time="20040513T082530+0000" data=" "85 by alanine were found in revertants of the mutant G85D. In contrast, all possible monosubstitutions in the mutated codon H92P were identified among the revertants of this mutant. The maturase activity of all novel forms of the protein is similar to the wild-type protein. [ABSTRACT FROM AUTHOR]

An optional group I intron was characterized at a single insertion point in nuclear small subunit rRNA (nuSSU rRNA) genes of the imperfect entomopathogenic fungi, Beauveria bassiana and B. brongniartii. Insertion points were conserved among nuSSU rRNA genes from 35 Beauveria isolates. PCR-RFLP and DNA sequencing identified 12 group I intron variants and were applied to the identification of strains isolated from insect hosts. Alignment of 383–404-nt subgroup IB3 group I introns indicated that four insertion/deletion (indel) mutations were the main basis of fragment length variation. Phylogeny reconstruction using parsimony and neighbor-joining methods suggested six lineages may be present among nuSSU rRNA group I intron sequences from Beauveria and related ascomycete fungi. Terminal node placement of Beauveria introns conflicted with previously published phylogenies constructed from gene sequences, suggesting horizontal transfer of group I introns. PCR-RFLP among introns provided a means for the differentiation of Beauveria isolates. [ABSTRACT FROM AUTHOR]

How group I introns originate in nuclear ribosomal (r)RNA genes is an important question in evolutionary biology. Central to this issue is the multitude of group I introns present in evolutionarily distantly related plant, fungal, and protist lineages, together with an understanding of their origin and lateral transfer from one exon to another, between cell organelles, and between cells. These introns vary considerably in primary and secondary structure; and their provenance from a few or perhaps many mobile elements that have spread in rRNAs is unknown. Here we show that a novel lineage of group IC1 introns inserted at position 516 (Escherichia coli gene numbering) in the small subunit rRNA in bangiophyte red algae and a brown alga (Aureoumbra lagunensis) are specifically related, although their host cells are not. These bangiophyte and Aureoumbra introns are the only known cases that have a helical insertion in the P5b helix. The highly conserved primary and secondary structure of the extra P5b helix suggests that it is important, although its specific function is unknown. Our study attempts to understand the origin and movement of these IC1 introns. [ABSTRACT FROM AUTHOR]

The second (bi2) intron of the mitochondrial cyt b gene from Saccharomyces capensis encodes a bifunctional protein which acts both as a maturase, promoting intron splicing, and as a homing-endonuclease, I-ScaI, promoting intron mobility. In this work we isolated and characterized revertants from a respiratory-deficient mutant in which both functions of the protein have been lost. Intragenic revertants resulted mainly from monosubstitutions in the mutated codon and in one case from a distant second site mutation. All novel variants of the S. capensis bi2 intron-encoded protein are competent for the maturase activity but only two of them can partially complement the homing function. [ABSTRACT FROM AUTHOR]

A mitochondrial cox3 gene in the alkane yeast, Yarrowia lipolytica, encodes a subunit-3 protein of cytochrome c oxidase, and contains a 1044 base-pair-long intron, as compared with the corresponding intronless gene in Saccharomyces cerevisiae. The intron belongs to a group I intron as determined by the cDNA sequence for the splicing sites as well as the predicted RNA secondary structure. Remarkably, this intron could code for a protein of 206 amino-acid residues which showed 63% similarity with an RNA maturase encoded by the second intron of the mitochondrial apocytochrome b gene in S. cerevisiae. Both introns occurred within the conserved exon sequence, 5′-TT(G/C)AGGTGC-3′, suggesting the possible transposition of a common ancestral intron. [ABSTRACT FROM AUTHOR]

The open reading frame of the first intron of the mitochondrial cox1 gene ( cox1I1) was expressed in Escherichia coli. The putative intron-encoded protein stimulated the formation of intra-chromosomal lac-recombinants about threefold. No stimulation was found when the reading frame was inserted in the opposite direction, or when it was interrupted by a deletion. The intronic open reading frame did not complement recA or recB mutants of E. coli. In S. pombe, elimination of this intron did not abolish homologous recombination in mitochondria. A possible role of the recombinase activity in yeast mitochondria will be discussed. [ABSTRACT FROM AUTHOR]