The complete mitochondrial DNA sequence of Hansenula wingei reveals new characteristics of yeast mitochondria

Sekito, Takayuki; Okamoto, Kozi; Kitano, Hiromichi; Yoshida, Kazuo

doi:10.1007/bf00311880

Cited by 55 publications

(46 citation statements)

References 38 publications

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“…Significant CRI and CRV matches turned up for the three known rnpB genes in S. cerevisiae , S. castellii (Petersen et al 2002), and A. nidulans (Lee et al 1996a), and four new candidates emerged in Pichia canadensis (Sekito et al 1995), Schizosaccharomyces pombe (Lang et al 1983), Schizosaccharomyces octosporus (Bullerwell et al 2003b), and Taphrina deformans, a fungus classified within Archiascomycota (or Taphrinomycetales, according to the National Center for Biotechnology Information [NCBI] nomenclature). Sequence alignments are shown in Figure 1.…”

Section: Search For Ascomycete Mitochondrial Rnpb Genesmentioning

confidence: 99%

Mitochondrial RNase P RNAs in ascomycete fungi: Lineage-specific variations in RNA secondary structure

Seif¹,

Forget²,

Martín³

et al. 2003

RNA

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The RNA subunit of mitochondrial RNase P (mtP-RNA) is encoded by a mitochondrial gene (rnpB) in several ascomycete fungi and in the protists Reclinomonas americana and Nephroselmis olivacea. By searching for universally conserved structural elements, we have identified previously unknown rnpB genes in the mitochondrial DNAs (mtDNAs) of two fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces octosporus; in the budding yeast Pichia canadensis; and in the archiascomycete Taphrina deformans. The expression of mtP-RNAs of the predicted size was experimentally confirmed in the two fission yeasts, and their precise 5 and 3 ends were determined by sequencing of cDNAs generated from circularized mtP-RNAs. Comparative RNA secondary structure modeling shows that in contrast to mtP-RNAs of the two protists R. americana and N. olivacea, those of ascomycete fungi all have highly reduced secondary structures. In certain budding yeasts, such as Saccharomycopsis fibuligera, we find only the two most conserved pairings, P1 and P4. A P18 pairing is conserved in Saccharomyces cerevisiae and its close relatives, whereas nearly half of the minimum bacterial consensus structure is retained in the RNAs of fission yeasts, Aspergillus nidulans and Taphrina deformans. The evolutionary implications of the reduction of mtP-RNA structures in ascomycetes will be discussed.

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Section: Search For Ascomycete Mitochondrial Rnpb Genesmentioning

confidence: 99%

Mitochondrial RNase P RNAs in ascomycete fungi: Lineage-specific variations in RNA secondary structure

Seif¹,

Forget²,

Martín³

et al. 2003

RNA

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“…Sequences (and accession numbers) used for the first data set were as follows: the metazoans Asterina pectinifera (D16387; Asakawa et al 1995), Balanoglossus carnosus (AF051097; Castresana et al 1998), Homo sapiens (X93334;Arnason, Xu, and Gullberg 1996), Drosophila melanogaster (U37541; Lewis, Farr, and Kaguni 1995), Katharina tunicata (U09810; Boore and Brown 1994), Lumbricus terrestris (U24570; Boore and Brown 1995), and Metridium senile (AF000023; Beagley, Okimoto, and Wolstenholme 1998); the fungi Allomyces macrogynus (U41288; Paquin and Lang 1996), Pichia canadensis, also known as Hansenula wingei (D31785; Sekito et al 1995), and Podospora anserina (X55026; Cummings et al. 1990); the plants Arabidopsis thaliana (Y08501 and Y08502; Unseld et al 1997) and Marchantia polymorpha (M68929; Oda et al 1992); the green alga Prototheca wickerhamii (U02970; Wolff et al 1994); the red alga Chondrus crispus (Z47547; Leblanc et al 1995); the amoeboid Acanthamoeba castellanii (U12386; Burger et al 1995); and the jacobid flagellate Reclinomonas americana (AF007261; Lang et al 1997).…”

Section: Sequences and Alignmentsmentioning

confidence: 99%

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

Castresana¹

2000

Molecular Biology and Evolution

8,972

6,134

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The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.

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“…This type of mtDNA architecture is now referred to as a circular-mapping mitochondrial genome (Jacobs et al 1996). The mitochondrial genomes of several yeast species have been sequenced completely (Lang 1984;Sekito et al 1995;Foury et al 1998;Kerscher et al 2001;Petersen et al 2002;Bullerwell et al 2003;Koszul et al 2003;Langkjaer et al 2003;Jones et al 2004) and presumably have similar structures. In contrast, the molecular architecture of the mtDNA of the petite negative yeast Candida parapsilosis is quite different.…”

Section: Introductionmentioning

confidence: 99%

Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis

et al. 2004

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The complete sequence of the mitochondrial DNA of the opportunistic yeast pathogen Candida parapsilosis was determined. The mitochondrial genome is represented by linear DNA molecules terminating with tandem repeats of a 738-bp unit. The number of repeats varies, thus generating a population of linear DNA molecules that are heterogeneous in size. The length of the shortest molecules is 30,922 bp, whereas the longer molecules have expanded terminal tandem arrays (nx738 bp). The mitochondrial genome is highly compact, with less than 8% of the sequence corresponding to non-coding intergenic spacers. In silico analysis predicted genes encoding fourteen protein subunits of complexes of the respiratory chain and ATP synthase, rRNAs of the large and small subunits of the mitochondrial ribosome, and twenty-four transfer RNAs. These genes are organized into two transcription units. In addition, six intronic ORFs coding for homologues of RNA maturase, reverse transcriptase and DNA endonucleases were identified. In contrast to its overall molecular architecture, the coding sequences of the linear mitochondrial DNA of C. parapsilosis are highly similar to their counterparts in the circular mitochondrial genome of its close relative C. albicans. The complete sequence has implications for both mitochondrial DNA replication and the evolution of linear DNA genomes.

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The complete mitochondrial DNA sequence of Hansenula wingei reveals new characteristics of yeast mitochondria

Cited by 55 publications

References 38 publications

Mitochondrial RNase P RNAs in ascomycete fungi: Lineage-specific variations in RNA secondary structure

Mitochondrial RNase P RNAs in ascomycete fungi: Lineage-specific variations in RNA secondary structure

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis

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