DNA splicing of mitochondrial group I and II introns in Schizosaccharomyces pombe

Merlos-Lange, Ana Maria; Kanbay, Feryal; Zimmer, Manfred; Wolf, Klaus

doi:10.1007/bf00333584

Cited by 29 publications

(4 citation statements)

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“…, hypergeometric test), including genes embedded within the group-II, self-spliced cox1 and cob1 introns (Merlos-Lange et al 1987). The corresponding lariat intermediates increased in dbr1D cells and were validated by lariat-specific RT-PCR, showing that these self-spliced introns also depend on Dbr1 in vivo (Supplemental Note 1).…”

Section: à15mentioning

confidence: 89%

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq

et al. 2014

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Both canonical and alternative splicing of RNAs are governed by intronic sequence elements and produce transient lariat structures fastened by branch points within introns. To map precisely the location of branch points on a genomic scale, we developed LaSSO (Lariat Sequence Site Origin), a data-driven algorithm which utilizes RNA-seq data. Using fission yeast cells lacking the debranching enzyme Dbr1, LaSSO not only accurately identified canonical splicing events, but also pinpointed novel, but rare, exon-skipping events, which may reflect aberrantly spliced transcripts. Compromised intron turnover perturbed gene regulation at multiple levels, including splicing and protein translation. Notably, Dbr1 function was also critical for the expression of mitochondrial genes and for the processing of self-spliced mitochondrial introns. LaSSO showed better sensitivity and accuracy than algorithms used for computational branch-point prediction or for empirical branch-point determination. Even when applied to a human data set acquired in the presence of debranching activity, LaSSO identified both canonical and exon-skipping branch points. LaSSO thus provides an effective approach for defining high-resolution maps of branch-site sequences and intronic elements on a genomic scale. LaSSO should be useful to validate introns and uncover branch-point sequences in any eukaryote, and it could be integrated into RNA-seq pipelines. [Supplemental material is available for this article.]Introns and exons refer to noncoding and coding sequences, respectively, that constitute protein-coding genes (Gilbert 1978). To create a functional messenger RNA (mRNA), introns are excised via a highly conserved and accurate process called splicing that culminates in concatenation of exon sequences into translatable transcripts. Splicing entails two transesterification reactions catalyzed by the spliceosome, a large RNA-protein complex (Wahl et al. 2009). The first reaction involves a nucleophilic attack of an adenosine (branch point) on the 59-splice donor, resulting in a lariat structure fixed by a 29-59 phosphodiester bond; the intron remains only attached to the downstream exon (Fig. 1A,B ;Padgett et al. 1985). The second reaction involves an attack of the detached upstream exon on the 39-splice acceptor, resulting in intron lariat release and exon ligation (Fig. 1C). The intron is then processed by exonucleolytic cleavage of the 39-lariat tail and linearization by the debranching enzyme Dbr1 (Fig.

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Section: à15mentioning

confidence: 89%

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq

et al. 2014

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“…However, in the case of the premature death syndrome in Podospora, the sequence similarity observed between the direct repeats (11- (41,42). Loss of introns at the DNA level was supposed to result from recombination involving a reverse-transcribed mature RNA (16,(43)(44)(45). In Podospora, examination of the sequence immediately upstream of the 5' end of the deletion showed that it contains potential intron binding sites (32) Fig.…”

Section: Discussionmentioning

confidence: 99%

A site-specific deletion in mitochondrial DNA of Podospora is under the control of nuclear genes.

Belcour

Begel

Picard

1991

Proc. Natl. Acad. Sci. U.S.A.

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In the filamentous fungus Podospora anserina, the association of two nuclear genes inevitably leads to a "premature death" phenotype consisting of an early end of vegetative growth a few days after ascospore germination. Mycelia showing this phenotype contain a mitochondrial chromosome that always bears the same deletion. One of the break points is exactly at the 5' splice site of a particular mitochondrial intron, suggesting that the deletion event could result from molecular mechanisms also involved in intron mobility.One of the nuclear genes involved in triggering this site-specific event belongs to the mating-type minus haplotype; the other is a mutant allele of a gene encoding a cytosolic ribosomal protein.In obligate aerobes, rearrangements of mitochondrial DNA (mtDNA) are responsible for various deleterious symptoms, such as maternally inherited male sterility in plants (1), several mycelial degenerative phenomena in fungi (2), and, as described more recently in humans, numerous neuromuscular (3) or hematological (4) diseases. In some cases, nuclear genes have been shown to control the mtDNA rearrangements (5, 6). The molecular mechanisms producing these rearrangements and the role played by nuclear-encoded proteins remain unclear in all cases.In the filamentous fungus Podospora anserina, vegetative growth is limited by a maternally inherited syndrome, called senescence, ending in cessation of mycelial elongation and apical cell death (7,8). In this species, senescence is clearly associated with mtDNA rearrangements and most probably is caused by them. More precisely, it has been shown that short mtDNA sequences are amplified as circular multimeric DNA molecules in senescent cultures (9)(10)(11)(12)(13)(14). It was shown that the most frequently amplified sequence corresponds exactly to a mitochondrial intron (15), intron a, and that most of the mutations allowing mycelia to escape senescence are rearrangements in intron a (12,(16)(17)(18). It has been known for a long time (19) that the nuclear genome controls the life-span of the fungus. For instance, the life-span of our reference strains differs according to their mating type: the process of senescence is delayed in mat+ strains compared with matones. However the differences, although significant, are not striking (see Table 1). Moreover the functions encoded by these genes are still unknown.The work presented here follows the observation that, in Podospora, mutations in several genes involved in the control of translational accuracy have an effect on the life-span (A. Raynal, personal communication; Table 1). As a first step, we focused our attention on the AS1-4 mutation. This particular allele confers a very long life-span to mat+ mycelia, while, when associated with mat-, it leads systematically to the premature death phenotype, consisting of an early end of mycelial growth a few days after ascospore germination.We showed that mycelia presenting this phenotype were in all cases heteroplasmic and that they systematically contained the same ...

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“…Many mitochondrial intronic mutants can revert frequently by clean deletion of the mutated intron, a process we have called in the past “DNA splicing”[1]. Introns can be deleted from the gene during the reversion of intronic mutations in Saccharomyces cerevisiae [1–5] and in Schizosaccharomyces pombe [6,7]. In the majority of revertants, we isolated from CYTb intron mutants, neighbouring safe introns are also deleted in a somewhat polar fashion: single bi1 intron deletions characterise revertants of bi1 mutants; (bi1, bi2) or (bi1, bi2, bi3) deletion characterise revertants of bi2 mutants; and the deletion of (bi1, bi2, bi3) introns is found exclusively in revertants of bi3 mutants.…”

Section: Introductionmentioning

confidence: 99%

The reverse transcriptase encoded by ai1 intron is active in the retro-deletion of yeast mitochondrial introns

Gargouri¹

2005

FEMS Yeast Research

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Genomic mitochondrial intron deletion occurs frequently during the reversion of mitochondrial intronic mutations in Saccharomyces cerevisiae. The multiplicity as well as the apparent polarity of intron deletion led us to propose the implication of reverse transcription in this process. The two first introns of the COX1 (cytochrome oxidase I) gene, ai1 and ai2, are known to be homologous to viral reverse transcriptase and to encode such activity. We have tested the involvement of these introns in the deletion process by constructing three isogenic strains. They contain the same reporter mutation in the second intron of the CYTb (cytochrome b) gene but differ from each other by the presence or the absence of the ai1 and/or ai2 introns in the other gene encoding the COX1 subunit. Only the strain lacking ai1 and ai2 introns is no more able to revert by intron deletion. The strain retaining only the ai1 intron was able to revert by intron deletion. We conclude that the reverse transcriptase activity, even when encoded by only ai1 intron, can act in trans in the intron deletion process, during the reversion of intronic mutations.

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DNA splicing of mitochondrial group I and II introns in Schizosaccharomyces pombe

Cited by 29 publications

References 25 publications

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq

A site-specific deletion in mitochondrial DNA of Podospora is under the control of nuclear genes.

The reverse transcriptase encoded by ai1 intron is active in the retro-deletion of yeast mitochondrial introns

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