<i>Mutator</i>
            -Like Element in the Yeast
            <i>Yarrowia lipolytica</i>
            Displays Multiple Alternative Splicings

Neuvéglise, Cécile; Chalvet, Fabienne; Wincker, Patrick; Gaillardin, Claude; Casarégola, Serge

doi:10.1128/ec.4.3.615-624.2005

Cited by 41 publications

(42 citation statements)

References 44 publications

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“…To identify transposable elements in this genome, we used the D. bruxellensis contigs as BLASTX queries against a database of protein sequences of TYA and TYB genes from Ty elements of multiple hemiascomycete species (43) and protein-coding regions of non-long terminal repeat (LTR) retrotransposons and DNA transposons from C. albicans and Y. lipolytica (12,25,44). Regions of the contigs that had hits with E values of Ͻ1e-10 to any of these proteins were counted as transposable elements.…”

Section: Methodsmentioning

confidence: 99%

“…The great majority of transposable elements so far described in hemiascomycete yeasts are LTR retrotransposons, although non-LTR retrotransposons and DNA transposons have been found in C. albicans and Y. lipolytica (12,25,44). The LTR retrotransposons fall into two broad categories: Ty1/copia (including Ty1, Ty2, T4, and Ty5 elements) and Ty3/gypsy (43).…”

Section: Vol 6 2007mentioning

confidence: 99%

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Genome Survey Sequencing of the Wine Spoilage YeastDekkera (Brettanomyces) bruxellensis

et al. 2007

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The hemiascomycete yeast Dekkera bruxellensis, also known as Brettanomyces bruxellensis, is a major cause of wine spoilage worldwide. Wines infected with D. bruxellensis develop distinctive, unpleasant aromas due to volatile phenols produced by this species, which is highly ethanol tolerant and facultatively anaerobic. Despite its importance, however, D. bruxellensis has been poorly genetically characterized until now. We performed genome survey sequencing of a wine strain of D. bruxellensis to obtain 0.4؋ coverage of the genome. We identified approximately 3,000 genes, whose products averaged 49% amino acid identity to their Saccharomyces cerevisiae orthologs, with similar intron contents. Maximum likelihood phylogenetic analyses suggest that the relationship between D. bruxellensis, S. cerevisiae, and Candida albicans is close to a trichotomy. The estimated rate of chromosomal rearrangement in D. bruxellensis is slower than that calculated for C. albicans, while its rate of amino acid evolution is somewhat higher. The proteome of D. bruxellensis is enriched for transporters and genes involved in nitrogen and lipid metabolism, among other functions, which may reflect adaptations to its low-nutrient, high-ethanol niche. We also identified an adenyl deaminase gene that has high similarity to a gene in bacteria of the Burkholderia cepacia species complex and appears to be the result of horizontal gene transfer. These data provide a resource for further analyses of the population genetics and evolution of D. bruxellensis and of the genetic bases of its physiological capabilities.

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Section: Methodsmentioning

confidence: 99%

Section: Vol 6 2007mentioning

confidence: 99%

Genome Survey Sequencing of the Wine Spoilage YeastDekkera (Brettanomyces) bruxellensis

et al. 2007

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“…By comparison, some eukaryotic genomes, such as those of S. cerevisiae and S. pombe, do not contain any DNA transposons, although they do contain retroelements. It is, however, not a rule in all ascomycetes, since Y. lipolytica and C. albicans contain several DNA transposons (366). Interestingly, it was shown that 100 to 200 copies of a MITE (miniature inverted-repeat transposable element)-type transposon in the rice genome, called Micron, was flanked by (TA) n repeats, suggesting that this transposon specifically targets a microsatellite (7).…”

Section: Dispersed Dna Repeatsmentioning

confidence: 99%

Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes

Richard

Kerrest

Dujon

2008

Microbiol Mol Biol Rev

491

411

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SUMMARY Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, “tandem repeats” and “dispersed repeats.” Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.

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“…TIR sequences appear to be important for element transposition and expression (Benito and Walbot, 1997;Raizada et al, 2001;Jiang et al, 2004). Recently, however, non-TIR MULEs have been reported in Arabidopsis (Arabidopsis thaliana), Lotus japonicus, maize, and yeast (Yarrowia lipolytica; Yu et al, 2000;Neuvéglise et al, 2005;Holligan et al, 2006;Wang and Dooner, 2006). Non-TIR MULEs refer to the MULEs with exceptionally short TIRs (less than 50 bp) and low similarity between the inverted terminal sequences.…”

mentioning

confidence: 99%

Selective Acquisition and Retention of Genomic Sequences by Pack-Mutator-Like Elements Based on Guanine-Cytosine Content and the Breadth of Expression

2013

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Mutator -Like Element in the Yeast Yarrowia lipolytica Displays Multiple Alternative Splicings

Cited by 41 publications

References 44 publications

Genome Survey Sequencing of the Wine Spoilage YeastDekkera (Brettanomyces) bruxellensis

Genome Survey Sequencing of the Wine Spoilage YeastDekkera (Brettanomyces) bruxellensis

Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes

Selective Acquisition and Retention of Genomic Sequences by Pack-Mutator-Like Elements Based on Guanine-Cytosine Content and the Breadth of Expression

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