The mitochondrial genomes of spontaneous orir petite mutants of yeast have rearranged repeat units organized as inverted tandem dimers

Faugeron-Fonty, Godeleine; Mangin, Marguerite; Huyard, A.; Bernardi, Giorgio

doi:10.1016/0378-1119(83)90131-2

Cited by 17 publications

(5 citation statements)

References 16 publications

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“…An even more complex situation may prevail in the spontaneous oriT petites (and in many of the ethidium bromideinduced petites), where repeat units are arranged as short inverted tandem dimers. In this case Faugeron-Fonty et al, 1983), we know from the very low suppressivity of oriT petites (<50o) that replication is extremely poor, since oriT genomes are competed out by wildtype genomes. Problems here might arise from the production of long transcripts starting at sequence r of the ori sequence in petites, but not in wild-type cells (see below), or from secondary structures formed between subsequent inverted repeats.…”

Section: Discussionmentioning

confidence: 99%

The initiation of DNA replication in the mitochondrial genome of yeast.

Baldacci¹,

Chérif-Zahar²,

Bernardi³

1984

The EMBO Journal

112

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We report here the first direct demonstration that the active ori sequences of the mitochondrial genome of Saccharomyces cerevisiae are indeed origins of DNA replication, as previously postulated on the basis of compelling but indirect evidence. Basically, such sequences are formed by four regions: (i) GC clusters A and B, which are separated by a 29‐bp AT stretch; (ii) a central 200‐bp AT stretch, l; (iii) GC cluster C; (iv) a 16‐bp AT stretch r, which comprises a site for transcription initiation. The ori sequences investigated, ori 1 and ori 5, have opposite orientations on the parental wild‐type genome; ori 1 has but ori 5 does not have an additional 14‐bp AT stretch r', between cluster C and sequence r; they were carried by the genomes of two spontaneous petites. In both ori sequences, nascent DNA chains using as template the strand containing sequence r (the ‘r strand’) start at the r end of cluster C, are elongated towards sequence l, and follow an RNA primer starting at sequence r. Nascent DNA chains copied on the ‘non‐r strand’ start within cluster C, are elongated towards sequence r, and follow an RNA primer starting in sequence l just before cluster C. Ori 1 and 5 are, therefore, used as sites for RNA‐primed bidirectional replication of mitochondrial DNA. Several aspects of this process are discussed.

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Section: Discussionmentioning

confidence: 99%

The initiation of DNA replication in the mitochondrial genome of yeast.

Baldacci¹,

Chérif-Zahar²,

Bernardi³

1984

The EMBO Journal

112

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“…Hints of the structures that we are describing as "mixed" structures have been commented on previously in ethidium bromide treated Petites (Locker et al, 1974;Locker et al, 1979) and spontaneous Petites (Heyting et al, 1979;Bos et al, 1980;Faugeron-Fonty et al, 1983). The first proposal of a model for the generation of these structures was provided in (Bos et al, 1980), but was subsequently refuted in (Faugeron-Fonty et al, 1983) where the claim was that these were larger ranging periodic structures produced by an unknown mechanism. However, our evidence of partially repeated units in Figure 5d, where two alignments are repeated with the same orientation but separated by an inverted alignment, precludes the structure proposed in (Faugeron-Fonty et al, 1983) and is evidence that adds to and is consistent with (Bos et al, 1980).…”

Section: Discussionmentioning

confidence: 78%

“…Here we also provide direct evidence for intramolecular and intermolecular heterogeneity in reporting "mixed" non-periodic structures in the mtDNA of yeast. Hints of the structures that we are describing as "mixed" structures have been commented on previously in ethidium bromide treated Petites (Locker et al, 1974;Locker et al, 1979) and spontaneous Petites (Heyting et al, 1979;Bos et al, 1980;Faugeron-Fonty et al, 1983). The first proposal of a model for the generation of these structures was provided in (Bos et al, 1980), but was subsequently refuted in (Faugeron-Fonty et al, 1983) where the claim was that these were larger ranging periodic structures produced by an unknown mechanism.…”

Section: Discussionmentioning

confidence: 78%

“…The first proposal of a model for the generation of these structures was provided in (Bos et al, 1980), but was subsequently refuted in (Faugeron-Fonty et al, 1983) where the claim was that these were larger ranging periodic structures produced by an unknown mechanism. However, our evidence of partially repeated units in Figure 5d, where two alignments are repeated with the same orientation but separated by an inverted alignment, precludes the structure proposed in (Faugeron-Fonty et al, 1983) and is evidence that adds to and is consistent with (Bos et al, 1980). As such, evidence presented here suggests the model presented in Figure 5e-f, based on the initial hypothesis in (Bos et al, 1980) is the appropriate model of generation of these "mixed" structures and that they are truly non-periodic.…”

Section: Discussionmentioning

confidence: 99%

“…Early studies of Petite mtDNA structure revealed that segments excised from the wild-type genome existed as tandem repeats in concatemer structures of various lengths (Locker et al, 1974;Locker et al, 1979;Faugeron-Fonty et al, 1979), with a few debated observations of nonperiodic structures (Heyting et al, 1979;Bos et al, 1980;Faugeron-Fonty et al, 1983). This led to a remarkable collection of work in structural genomics that detailed the excision mechanismsequence-specific illegitimate recombination within and between abundant repeated AT regions and GC clusters in non-coding regions (Bernardi et al, 1976;Marotta et al, 1982;de Zamaroczy et al, 1983).…”

Section: Introductionmentioning

confidence: 99%

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Contingency and selection in mitochondrial genome dynamics

Nunn

Goyal

2021

Preprint

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Eukaryotic cells contain numerous copies of mitochondrial DNA (mtDNA), allowing for the coexistence of mutant and wild-type mtDNA in individual cells. The fate of mutant mtDNA depends on their relative replicative fitness within cells and the resulting cellular fitness within populations of cells. Yet the dynamics of the generation of mutant mtDNA and features that inform their fitness remain unaddressed. Here we utilize long read single-molecule sequencing to track mtDNA mutational trajectories in Saccharomyces cerevisiae. We show a previously unseen pattern that constrains subsequent excision events in mtDNA fragmentation. We also provide evidence for the generation of rare and contentious non-periodic mtDNA structures that lead to persistent diversity within individual cells. Finally, we show that measurements of relative fitness of mtDNA fit a phenomenological model that highlights important biophysical parameters governing mtDNA fitness. Altogether, our study provides techniques and insights into the dynamics of large structural changes in genomes that may be applicable in more complex organisms.

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Polymorphic variations in the ori sequences from the mitochondrial genomes of different wild-type yeast strains

Faugeron-Fonty

Goyon

1985

Curr Genet

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We determined the restriction maps and primary structures of two as yet poorly characterized regions of the mitochondrial genomes of different wild-type strains of Saccharomyces cerevisiae. These regions respectively comprised the ori1 sequence and the newly identified ori8 sequence. Ori1 and ori8, together with their flanking sequences, exhibit a large polymorphism, resulting from specific variations due to insertions or deletions of optional GC clusters at different locations. The mechanisms underlying such sequence rearrangements are discussed.

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The mitochondrial genomes of spontaneous orir petite mutants of yeast have rearranged repeat units organized as inverted tandem dimers

Cited by 17 publications

References 16 publications

The initiation of DNA replication in the mitochondrial genome of yeast.

The initiation of DNA replication in the mitochondrial genome of yeast.

Contingency and selection in mitochondrial genome dynamics

Polymorphic variations in the ori sequences from the mitochondrial genomes of different wild-type yeast strains

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