A comparative study of the ori sequences from the mitochondrial genomes of twenty wild-type yeast strains

Faugeron-Fonty, Godeleine; Kim, Caroline Le Van; Zamaroczy, Miklos de; Goursot, Regina; Bernardi, Giorgio

doi:10.1016/0378-1119(84)90020-9

Cited by 30 publications

(12 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Eight yeast mitochondrial origins of replication ( ori ) have been proposed, although not all of the ori are active, and those that are active are strain dependent[48]. Our bioinformatic analysis of the S288C mitochondrial DNA sequence shows that 3 ori are immediately downstream of the 20-base promoter and conform to a 5-part consensus sequence (Figure 2A).…”

Section: Resultsmentioning

confidence: 91%

The Mitochondrial RNA Landscape of Saccharomyces cerevisiae

et al. 2013

View full text Add to dashboard Cite

Mitochondria are essential organelles that harbor a reduced genome, and expression of that genome requires regulated metabolism of its transcriptome by nuclear-encoded proteins. Despite extensive investigation, a comprehensive map of the yeast mitochondrial transcriptome has not been developed and all of the RNA-metabolizing proteins have not been identified, both of which are prerequisites to elucidating the basic RNA biology of mitochondria. Here, we present a mitochondrial transcriptome map of the yeast S288C reference strain. Using RNAseq and bioinformatics, we show the expression level of all transcripts, revise all promoter, origin of replication, and tRNA annotations, and demonstrate for the first time the existence of alternative splicing, mirror RNAs, and a novel RNA processing site in yeast mitochondria. The transcriptome map has revealed new aspects of mitochondrial RNA biology and we expect it will serve as a valuable resource. As a complement to the map, we present our compilation of all known yeast nuclear-encoded ribonucleases (RNases), and a screen of this dataset for those that are imported into mitochondria. We sought to identify RNases that are refractory to recovery in traditional mitochondrial screens due to an essential function or eclipsed accumulation in another cellular compartment. Using this in silico approach, the essential RNase of the nuclear and cytoplasmic exosome, Dis3p, emerges as a strong candidate. Bioinformatics and in vivo analyses show that Dis3p has a conserved and functional mitochondrial-targeting signal (MTS). A clean and marker-less chromosomal deletion of the Dis3p MTS results in a defect in the decay of intron and mirror RNAs, thus revealing a role for Dis3p in mitochondrial RNA decay.

show abstract

Section: Resultsmentioning

confidence: 91%

The Mitochondrial RNA Landscape of Saccharomyces cerevisiae

et al. 2013

View full text Add to dashboard Cite

show abstract

“…DISCUSSION A subset of yeast mitochondrial promoters is located immediately adjacent to putative origins of replication; as such, they have been implicated in priming of DNA replication. A common feature of these replication origins is the presence of a short guanosine-rich region (GC cluster C/CSB II-like element) in the priming strand downstream of the transcription start site (1,10,13,26). This situation is similar to that for the vertebrate mtDNA leading-strand origin and suggests possible functional relationships between the yeast on/rep and vertebrate origin systems.…”

Section: Resultsmentioning

confidence: 99%

“…However, studies with hypersuppressive petite strains indicate that putative yeast mitochondrial replication origins (on [or rep {reference 12 and references therein}] sequences) are characterized by a 300-bp A+T-rich segment containing the following regions: a 16-bp A+T-rich sequence containing an active promoter for transcription initiation (termed r), a 17-bp GC cluster C located immediately downstream of the promoter, a central 200-bp A+T-rich stretch (termed C), and GC clusters A and B, which are separated by an A+T-rich region (1,10,13 (1,10,26). These include the existence of a functional promoter at or near the site of transition from RNA to DNA synthesis; the presence of a short, conserved G-rich sequence block at the origin (GC cluster C/CSB II [10,13]); and the occurrence of an additional conserved element, CSB I, in this region (10,13). However (4).…”

mentioning

confidence: 99%

Saccharomyces cerevisiae contains an RNase MRP that cleaves at a conserved mitochondrial RNA sequence implicated in replication priming.

Stohl

Clayton

1992

Mol. Cell. Biol.

View full text Add to dashboard Cite

The overall mode of mitochondrial DNA (mtDNA) replication is best understood for the mouse and human systems, and a general model of vertebrate mtDNA replication has been established (9). Mammalian mtDNA replicates by unidirectional synthesis from two distinct origins, the origin of heavy-strand replication and the origin of light-strand replication, which are located two-thirds of the genomic distance apart on the closed circle. The structural features and mechanisms of RNA priming are very different at these two origins (3,7,9,29,30). A characteristic hallmark of the origin of heavy-strand replication is the presence of three evolutionarily conserved sequence blocks (CSBs I, II, and III) at or near the 5' ends of newly synthesized heavy strands. It has been demonstrated for nearly all 5' ends of nascent heavy-strand DNAs that there are RNA species whose 3' ends map immediately adjacent to the DNA 5' ends. It has also been shown that 5' ends of these RNAs map at the initiation site of transcription from the major lightstrand promoter (3, 7). On the basis of these and other findings, Chang and coworkers hypothesized that transcripts from this promoter play a role in heavy-strand replication by serving as primers for DNA synthesis and that individual primer termini were generated by processing of a primary transcript (3, 7).Mammalian complementary to the origin of leading heavy-strand mtDNA replication (4, 6, 28). The endonuclease activity is present in both nuclear and mitochondrial fractions (2,5,14,17,28) and has been proposed to participate in mitochondrial primer RNA metabolism in vivo. The standard mitochondrial RNA (mtRNA) substrate for mouse and human RNase MRPs contains three short regions of sequence that are highly conserved in vertebrate species (CSBs I, II, and III). Initial characterization of the mouse RNase MRP activity demonstrated that the site-specific cleavage of mtRNA substrate in vitro occurred immediately adjacent to CSB II, and it was postulated that CSB II played a role in cleavage site specificity (4). Subsequent deletional analysis and saturation mutagenesis have determined basic substrate requirements for cleavage by mouse RNase MRP; CSB II and CSB III are essential for both efficient and accurate cleavage, whereas CSB I is not (2).In contrast to the mammalian system, our knowledge of yeast wild-type mtDNA replication initiation, at the molecular level, is less advanced. However, studies with hypersuppressive petite strains indicate that putative yeast mitochondrial replication origins (on [or rep {reference 12 and references therein}] sequences) are characterized by a 300-bp A+T-rich segment containing the following regions: a 16-bp A+T-rich sequence containing an active promoter for transcription initiation (termed r), a 17-bp GC cluster C located immediately downstream of the promoter, a central 200-bp A+T-rich stretch (termed C), and GC clusters A and B, which are separated by an A+T-rich region (1, 10, 13). It has also been proposed that the active on sequences of yeast mtDNA are ...

show abstract

“…Our laboratory has determined the number, the location, the orientation and the primary structure of the ori sequences present in the mitochondrial genome of wild-type Saccharomyces cerevisiae (Figure 1; de Zamaroczy et al, 1979de Zamaroczy et al, , 1981Goursot et al, 1980;Bemardi et al, 1980;Bernardi, 1982;Faugeron-Fonty et al, 1984). So far, evidence for the involvement of ori sequences in DNA replication rests: (i) on their expected presence in the repeat units of the vast majority of spontaneous petites; (ii) on the correlation between the intact or altered state of the ori sequence and the level of transmission of the petite mitochondrial genome to the progeny of crosses with wild-type cells; (iii) on the expected association between the sites of initiation of DNA replication and RNA transcription; and (iv) on their similarity with bona fide replication origins.…”

Section: Introductionmentioning

confidence: 99%

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

Baldacci¹,

Chérif-Zahar²,

Bernardi³

1984

The EMBO Journal

112

View full text Add to dashboard Cite

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.

show abstract

A comparative study of the ori sequences from the mitochondrial genomes of twenty wild-type yeast strains

Cited by 30 publications

References 34 publications

The Mitochondrial RNA Landscape of Saccharomyces cerevisiae

The Mitochondrial RNA Landscape of Saccharomyces cerevisiae

Saccharomyces cerevisiae contains an RNase MRP that cleaves at a conserved mitochondrial RNA sequence implicated in replication priming.

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

Contact Info

Product

Resources

About