Mobile Introns Shape the Genetic Diversity of Their Host Genes

Repar, Jelena; Warnecke, Tobias

doi:10.1534/genetics.116.199059

Cited by 42 publications

(43 citation statements)

References 46 publications

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“…Nonetheless, the species Acremonium fuci, A. chrysogenum and Clonostachys rosea presented the gene cox2 displaced, while Nectria cinnabarina and Epichloe typhina displayed a rearrangement for the nad4l gene. Differences in genome ordering can be attributed due to non-homologous recombination processes, plasmid sequence integration or presence of transposable elements, such as IGI sequences and HEGs (Gordenin et al, 1993;Lavrov et al, 2002;Rocha, 2003;Repar and Warnecke, 2017).…”

Section: Discussionmentioning

confidence: 99%

Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes

et al. 2020

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Divergence Time and Mitogenome Shaping and investigated its relationship with coding and non-coding elements as well as with the length of mitogenomes. Altogether, our results demonstrated that introns and HEGs are key elements on mitogenome shaping and its presence on fast-evolving mtDNAs could be mostly explained by its divergence time, although the intron sharing profile suggests the involvement of other mechanisms on the mitochondrial genome evolution, such as horizontal transference.

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Section: Discussionmentioning

confidence: 99%

Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes

et al. 2020

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“…The vast diversity in the S. cerevisiae mitochondrial genomes in our study population included size, intron content, and copy number variation, as well as SNPs/indels in the 36 core genes [RNA-encoding (n = 27): 21S, 15S, RPM1, 24 tRNAs; protein-encoding (n = 9): VAR1, COX1, COX2, COX3, COB, ATP6, ATP8, OLI1, RF1]. Some aspects of these S. cerevisiae mitochondrial genomes have been previously described (Wolters et al 2015;Peris et al 2017;Repar and Warnecke 2017). Therefore, we focus this discussion on the novel ENS2 and ATP6 genotype-oligomycin phenotype associations; ENS2 and ATP6 phylogenies and introgression; Ens2-mediated recombination; the identification and characterization of mitochondrial genotype-dependent phenotypes in iso-nuclear F1 pairs; and nuclear-mitochondrial epistasis, as well as its implications for the analysis of quantitative traits.…”

Section: Discussionmentioning

confidence: 99%

Mitochondrial Genome Variation Affects Multiple Respiration and Nonrespiration Phenotypes in Saccharomyces cerevisiae

et al. 2018

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Mitochondrial genome variation and its effects on phenotypes have been widely analyzed in higher eukaryotes but less so in the model eukaryote Saccharomyces cerevisiae. Here, we describe mitochondrial genome variation in 96 diverse S. cerevisiae strains and assess associations between mitochondrial genotype and phenotypes as well as nuclear-mitochondrial epistasis. We associate sensitivity to the ATP synthase inhibitor oligomycin with SNPs in the mitochondrially encoded ATP6 gene. We describe the use of isonuclear F1 pairs, the mitochondrial genome equivalent of reciprocal hemizygosity analysis, to identify and analyze mitochondrial genotype-dependent phenotypes. Using iso-nuclear F1 pairs, we analyze the oligomycin phenotype-ATP6 association and find extensive nuclear-mitochondrial epistasis. Similarly, in iso-nuclear F1 pairs, we identify many additional mitochondrial genotype-dependent respiration phenotypes, for which there was no association in the 96 strains, and again find extensive nuclear-mitochondrial epistasis that likely contributes to the lack of association in the 96 strains. Finally, in iso-nuclear F1 pairs, we identify novel mitochondrial genotype-dependent nonrespiration phenotypes: resistance to cycloheximide, ketoconazole, and copper. We discuss potential mechanisms and the implications of mitochondrial genotype and of nuclear-mitochondrial epistasis effects on respiratory and nonrespiratory quantitative traits.

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“…In contrast to other mobile elements, self-splicing introns do not spawn a large pool of copies that disperse across the genome to escape mutational erasure. Rather, owing to highly specific homing sites, each intron is typically confined to a single location in the host genome and evolutionary persistence seems to rely on continued re-invasion, either from other individuals in the same population ( Goddard and Burt, 1999 ) or across species boundaries ( Skelly and Maleszka, 1991 ; Dujon, 1989 ; Repar and Warnecke, 2017 ). Self-splicing introns can spread despite considerable fitness costs to the host ( Hickey, 1982 ).…”

Section: Introductionmentioning

confidence: 99%

Normal mitochondrial function in Saccharomyces cerevisiae has become dependent on inefficient splicing

Rudan

Dib

Musa

et al. 2018

eLife

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Self-splicing introns are mobile elements that have invaded a number of highly conserved genes in prokaryotic and organellar genomes. Here, we show that deletion of these selfish elements from the Saccharomyces cerevisiae mitochondrial genome is stressful to the host. A strain without mitochondrial introns displays hallmarks of the retrograde response, with altered mitochondrial morphology, gene expression and metabolism impacting growth and lifespan. Deletion of the complete suite of mitochondrial introns is phenocopied by overexpression of the splicing factor Mss116. We show that, in both cases, abnormally efficient transcript maturation results in excess levels of mature cob and cox1 host mRNA. Thus, inefficient splicing has become an integral part of normal mitochondrial gene expression. We propose that the persistence of S. cerevisiae self-splicing introns has been facilitated by an evolutionary lock-in event, where the host genome adapted to primordial invasion in a way that incidentally rendered subsequent intron loss deleterious.

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Mobile Introns Shape the Genetic Diversity of Their Host Genes

Abstract: Self-splicing introns populate several highly conserved protein-coding genes in fungal and plant mitochondria. In fungi, many of these introns have...

Cited by 42 publications

References 46 publications

Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes

Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes

Mitochondrial Genome Variation Affects Multiple Respiration and Nonrespiration Phenotypes in Saccharomyces cerevisiae

Normal mitochondrial function in Saccharomyces cerevisiae has become dependent on inefficient splicing

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