The secondary structure and phylogenetic relationship deduced from complete nucleotide sequence of mitochondrial small subunit rRNA in yeast Hansenula wingei.

Okamoto, Kozi; Sekito, Takayuki; Yoshida, Kazuo

doi:10.1266/ggs.71.69

Cited by 8 publications

(2 citation statements)

References 25 publications

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“…2). Interestingly enough, these helices which are stably present in most other fungal homologs (Gutell et al , 1985; Okamoto et al , 1996; Hegedus et al , 1998) are modified in a similar way as in reduced rns counterparts from other lineages such as metazoan and certain protists (Gray et al , 1998; Boore, 1999; Cannone et al , 2002). The complete absence of helix 43 is also noticeable, a vestige of which appears even in the Caenorhabditis elegans rns , the smallest rRNA sequence known among Metazoa (697 bp; Mears et al , 2002).…”

Section: Resultsmentioning

confidence: 98%

The mitochondrial genome of the wine yeastHanseniaspora uvarum: a unique genome organization among yeast/fungal counterparts

Pramateftaki

Kouvelis

Lanaridis

et al. 2006

FEMS Yeast Research

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The complete sequence of the apiculate wine yeast Hanseniaspora uvarum mtDNA has been determined and analysed. It is an extremely compact linear molecule containing the shortest functional region ever found in fungi (11 094 bp long), flanked by Type 2 telomeric inverted repeats. The latter contained a 2704-bp-long subterminal region and tandem repeats of 839-bp units. In consequence, a population of mtDNA molecules that differed at the number of their telomeric reiterations was detected. The functional region of the mitochondrial genome coded for 32 genes, which included seven subunits of respiratory complexes and ATP synthase (the genes encoding for NADH oxidoreductase subunits were absent), two rRNAs and 23 tRNA genes which recognized codons for all amino acids. A single intron interrupted the cytochrome oxidase subunit 1 gene. A number of reasons contributed towards its strikingly small size, namely: (1) the remarkable size reduction (by >40%) of the rns and rnl genes; (2) that most tRNA genes and five of the seven protein-coding genes were the shortest among known yeast homologs; and (3) that the noncoding regions were restricted to 5.1% of the genome. In addition, the genome showed multiple changes in the orientation of transcription and the gene order differed drastically from other yeasts. When all protein coding gene sequences were considered as one unit and were compared with the corresponding molecules from all other complete mtDNAs of yeasts, the phylogenetic trees constructed robustly supported its placement basal to the yeast species of the 'Saccharomyces complex', demonstrating the advantage of this approach over single-gene or multigene approaches of unlinked genes.

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Section: Resultsmentioning

confidence: 98%

The mitochondrial genome of the wine yeastHanseniaspora uvarum: a unique genome organization among yeast/fungal counterparts

Pramateftaki

Kouvelis

Lanaridis

et al. 2006

FEMS Yeast Research

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“…Beside the cox1 gene, the small sub-unit rDNA gene (SSU-rDNA) constitutes interesting molecules by his important evolutionary dimension and structural complexity (Okamoto et al 1996). This gene consists of regions with varying degrees of sequence divergence, divided into the highly conserved core interrupted by nine domains with large length variations (Neefs et al, 1993).…”

Section: Introductionmentioning

confidence: 99%

Molecular evolution of mitochondrial ribosomal DNA in the fungal genus Tricholoma: Barcoding implications

Mouhamadou

Carriconde

Gryta

et al. 2008

Fungal Genetics and Biology

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Secondary Structure and Molecular Evolution of the Mitochondrial Small Subunit Ribosomal RNA in Agaricales (Euagarics clade, Homobasidiomycota)

Barroso¹,

Sirand‐Pugnet²,

Mouhamadou³

et al. 2003

Journal of Molecular Evolution

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The complete sequences and secondary structures of the mitochondrial small subunit (SSU) ribosomal RNAs of both mostly cultivated mushrooms Agaricus bisporus (1930 nt) and Lentinula edodes (2164 nt) were achieved. These secondary structures and that of Schizophyllum commune (1872 nt) were compared to that previously established for Agrocybe aegerita. The four structures are near the model established for Archae, Bacteria, plastids, and mitochondria; particularly the helices 23 and 37, described as specific to bacteria, are present. Within the four Agaricales (Homobasidiomycota), the SSU-rRNA "core" is conserved in size (966 to 1009 nt) with the exception of an unusual extension of 40 nt in the H17 helix of S. commune. The four core sequences possess 76% of conserved positions and a cluster of C in their 3' end, which could constitute a signal involved in the RNA maturation process. Among the nine putative variable domains, three (V3, V5, V7) do not show significant length variations and possess similar percentages of conserved positions (69%) than the core. The other six variable domains show important length variations, due to independent large size inserted/deleted sequences, and higher rates of nucleotide substitutions than the core (only 31% of conserved positions between the four species). Interestingly, the inserted/deleted sequences are located in few preferential sites (hot spots for insertion/deletion) where they seem to arise or disappear haphazardly during evolution. These sites are located on the surface of the tertiary structure of the 30S ribosomal subunit, at the beginning of hairpin loops; the insertions lead to a lengthening of existing hairpins or to branching loops bearing up to five additional helices.

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The secondary structure and phylogenetic relationship deduced from complete nucleotide sequence of mitochondrial small subunit rRNA in yeast Hansenula wingei.

Cited by 8 publications

References 25 publications

The mitochondrial genome of the wine yeastHanseniaspora uvarum: a unique genome organization among yeast/fungal counterparts

The mitochondrial genome of the wine yeastHanseniaspora uvarum: a unique genome organization among yeast/fungal counterparts

Molecular evolution of mitochondrial ribosomal DNA in the fungal genus Tricholoma: Barcoding implications

Secondary Structure and Molecular Evolution of the Mitochondrial Small Subunit Ribosomal RNA in Agaricales (Euagarics clade, Homobasidiomycota)

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