Micheline Wésolowski-Louvel
University of Lyon
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Featured researches published by Micheline Wésolowski-Louvel.
Nature | 2004
Bernard Dujon; David James Sherman; Gilles Fischer; Pascal Durrens; Serge Casaregola; Ingrid Lafontaine; Jacky de Montigny; Christian Marck; Cécile Neuvéglise; Emmanuel Talla; Nicolas Goffard; Lionel Frangeul; Michel Aigle; Véronique Anthouard; Anna Babour; Valérie Barbe; Stéphanie Barnay; Sylvie Blanchin; Jean-Marie Beckerich; Emmanuelle Beyne; Claudine Bleykasten; Anita Boisramé; Jeanne Boyer; Laurence Cattolico; Fabrice Confanioleri; Antoine de Daruvar; Laurence Despons; Emmanuelle Fabre; Cécile Fairhead; Hélène Ferry-Dumazet
Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.
FEBS Letters | 2000
Jean-Luc Souciet; Michel Aigle; François Artiguenave; Gaëlle Blandin; Monique Bolotin-Fukuhara; Elisabeth Bon; Serge Casaregola; Jacky de Montigny; Bernard Dujon; Pascal Durrens; Claude Gaillardin; Andrée Lépingle; Bertrand Llorente; Alain Malpertuy; Cécile Neuvéglise; Odile Ozier-Kalogeropoulos; Serge Potier; William Saurin; Fredj Tekaia; Claire Toffano-Nioche; Micheline Wésolowski-Louvel; Patrick Wincker; Jean Weissenbach
The identification of molecular evolutionary mechanisms in eukaryotes is approached by a comparative genomics study of a homogeneous group of species classified as Hemiascomycetes. This group includes Saccharomyces cerevisiae, the first eukaryotic genome entirely sequenced, back in 1996. A random sequencing analysis has been performed on 13 different species sharing a small genome size and a low frequency of introns. Detailed information is provided in the 20 following papers. Additional tables available on websites describe the ca. 20 000 newly identified genes. This wealth of data, so far unique among eukaryotes, allowed us to examine the conservation of chromosome maps, to identify the ‘yeast‐specific’ genes, and to review the distribution of gene families into functional classes. This project conducted by a network of seven French laboratories has been designated ‘Génolevures’.
The ISME Journal | 2007
Julie Bailly; Laurence Fraissinet-Tachet; Marie-Christine Verner; Jean-Claude Debaud; Marc Lemaire; Micheline Wésolowski-Louvel; Roland Marmeisse
To appreciate the functional diversity of communities of soil eukaryotic micro-organisms we evaluated an experimental approach based on the construction and screening of a cDNA library using polyadenylated mRNA extracted from a forest soil. Such a library contains genes that are expressed by each of the different organisms forming the community and represents its metatranscriptome. The diversity of the organisms that contributed to this library was evaluated by sequencing a portion of the 18S rDNA gene amplified from either soil DNA or reverse-transcribed RNA. More than 70% of the sequences were from fungi and unicellular eukaryotes (protists) while the other most represented group was the metazoa. Calculation of richness estimators suggested that more than 180 species could be present in the soil samples studied. Sequencing of 119 cDNA identified genes with no homologues in databases (32%) and genes coding proteins involved in different biochemical and cellular processes. Surprisingly, the taxonomic distribution of the cDNA and of the 18S rDNA genes did not coincide, with a marked under-representation of the protists among the cDNA. Specific genes from such an environmental cDNA library could be isolated by expression in a heterologous microbial host, Saccharomyces cerevisiae. This is illustrated by the functional complementation of a histidine auxotrophic yeast mutant by two cDNA originating possibly from an ascomycete and a basidiomycete fungal species. Study of the metatranscriptome has the potential to uncover adaptations of whole microbial communities to local environmental conditions. It also gives access to an abundant source of genes of biotechnological interest.
FEBS Letters | 2000
Gaëlle Blandin; Pascal Durrens; Fredj Tekaia; Michel Aigle; Monique Bolotin-Fukuhara; Elisabeth Bon; Serge Casaregola; Jacky de Montigny; Claude Gaillardin; Andrée Lépingle; Bertrand Llorente; Alain Malpertuy; Cécile Neuvéglise; Odile Ozier-Kalogeropoulos; Arnaud Perrin; Serge Potier; Jean-Luc Souciet; Emmanuel Talla; Claire Toffano-Nioche; Micheline Wésolowski-Louvel; Christian Marck; Bernard Dujon
Since its completion more than 4 years ago, the sequence of Saccharomyces cerevisiae has been extensively used and studied. The original sequence has received a few corrections, and the identification of genes has been completed, thanks in particular to transcriptome analyses and to specialized studies on introns, tRNA genes, transposons or multigene families. In order to undertake the extensive comparative sequence analysis of this program, we have entirely revisited the S. cerevisiae sequence using the same criteria for all 16 chromosomes and taking into account publicly available annotations for genes and elements that cannot be predicted. Comparison with the other yeast species of this program indicates the existence of 50 novel genes in segments previously considered as ‘intergenic’ and suggests extensions for 26 of the previously annotated genes.
FEBS Letters | 2000
Bertrand Llorente; Alain Malpertuy; Cécile Neuvéglise; Jacky de Montigny; Michel Aigle; François Artiguenave; Gaëlle Blandin; Monique Bolotin-Fukuhara; Elisabeth Bon; Serge Casaregola; Pascal Durrens; Claude Gaillardin; Andrée Lépingle; Odile Ozier-Kalogeropoulos; Serge Potier; William Saurin; Fredj Tekaia; Claire Toffano-Nioche; Micheline Wésolowski-Louvel; Patrick Wincker; Jean Weissenbach; Jean-Luc Souciet; Bernard Dujon
We have analyzed the evolution of chromosome maps of Hemiascomycetes by comparing gene order and orientation of the 13 yeast species partially sequenced in this program with the genome map of Saccharomyces cerevisiae. From the analysis of nearly 8000 situations in which two distinct genes having homologs in S. cerevisiae could be identified on the sequenced inserts of another yeast species, we have quantified the loss of synteny, the frequency of single gene deletion and the occurrence of gene inversion. Traces of ancestral duplications in the genome of S. cerevisiae could be identified from the comparison with the other species that do not entirely coincide with those identified from the comparison of S. cerevisiae with itself. From such duplications and from the correlation observed between gene inversion and loss of synteny, a model is proposed for the molecular evolution of Hemiascomycetes. This model, which can possibly be extended to other eukaryotes, is based on the reiteration of events of duplication of chromosome segments, creating transient merodiploids that are subsequently resolved by single gene deletion events.
FEBS Letters | 2000
Monique Bolotin-Fukuhara; Claire Toffano-Nioche; François Artiguenave; Guillemette Duchateau-Nguyen; Marc Lemaire; Roland Marmeisse; Robert Montrocher; Catherine Robert; Michel Termier; Patrick Wincker; Micheline Wésolowski-Louvel
Random sequencing of the Kluyveromyces lactis genome allowed the identification of 2235–2601 open reading frames (ORFs) homologous to S. cerevisiae ORFs, 51 ORFs which were homologous to genes from other species, 64 tRNAs, the complete rDNA repeat, and a few Ty1‐ and Ty2‐like sequences. In addition, the complete sequence of plasmid pKD1 and a large coverage of the mitochondrial genome were obtained. The global distribution into general functional categories found in Saccharomyces cerevisiae and as defined by MIPS is well conserved in K. lactis. However, detailed examination of certain subcategories revealed a small excess of genes involved in amino acid metabolism in K. lactis. The sequences are deposited at EMBL under the accession numbers AL424881–AL430960.
FEBS Letters | 2000
Bertrand Llorente; Pascal Durrens; Alain Malpertuy; Michel Aigle; François Artiguenave; Gaëlle Blandin; Monique Bolotin-Fukuhara; Elisabeth Bon; Serge Casaregola; Bernard Dujon; Jacky de Montigny; Andrée Lépingle; Cécile Neuvéglise; Odile Ozier-Kalogeropoulos; Serge Potier; William Saurin; Fredj Tekaia; Claire Toffano-Nioche; Micheline Wésolowski-Louvel; Patrick Wincker; Jean Weissenbach; Jean-Luc Souciet; Claude Gaillardin
We have evaluated the degree of gene redundancy in the nuclear genomes of 13 hemiascomycetous yeast species. Saccharomyces cerevisiae singletons and gene families appear generally conserved in these species as singletons and families of similar size, respectively. Variations of the number of homologues with respect to that expected affect from 7 to less than 24% of each genome. Since S. cerevisiae homologues represent the majority of the genes identified in the genomes studied, the overall degree of gene redundancy seems conserved across all species. This is best explained by a dynamic equilibrium resulting from numerous events of gene duplication and deletion rather than by a massive duplication event occurring in some lineages and not in others.
FEBS Letters | 2000
Alain Malpertuy; Fredj Tekaia; Serge Casaregola; Michel Aigle; François Artiguenave; Gaëlle Blandin; Monique Bolotin-Fukuhara; Elisabeth Bon; Jacky de Montigny; Pascal Durrens; Claude Gaillardin; Andrée Lépingle; Bertrand Llorente; Cécile Neuvéglise; Odile Ozier-Kalogeropoulos; Serge Potier; William Saurin; Claire Toffano-Nioche; Micheline Wésolowski-Louvel; Patrick Wincker; Jean Weissenbach; Jean-Luc Souciet; Bernard Dujon
Comparisons of the 6213 predicted Saccharomyces cerevisiae open reading frame (ORF) products with sequences from organisms of other biological phyla differentiate genes commonly conserved in evolution from ‘maverick’ genes which have no homologue in phyla other than the Ascomycetes. We show that a majority of the ‘maverick’ genes have homologues among other yeast species and thus define a set of 1892 genes that, from sequence comparisons, appear ‘Ascomycetes‐specific’. We estimate, retrospectively, that the S. cerevisiae genome contains 5651 actual protein‐coding genes, 50 of which were identified for the first time in this work, and that the present public databases contain 612 predicted ORFs that are not real genes. Interestingly, the sequences of the ‘Ascomycetes‐specific’ genes tend to diverge more rapidly in evolution than that of other genes. Half of the ‘Ascomycetes‐specific’ genes are functionally characterized in S. cerevisiae, and a few functional categories are over‐represented in them.
FEBS Letters | 2000
Fredj Tekaia; Gaëlle Blandin; Alain Malpertuy; Bertrand Llorente; Pascal Durrens; Claire Toffano-Nioche; Odile Ozier-Kalogeropoulos; Elisabeth Bon; Claude Gaillardin; Michel Aigle; Monique Bolotin-Fukuhara; Serge Casaregola; Jacky de Montigny; Andrée Lépingle; Cécile Neuvéglise; Serge Potier; Jean-Luc Souciet; Micheline Wésolowski-Louvel; Bernard Dujon
The primary analysis of the sequences for our Hemiascomycete random sequence tag (RST) project was performed using a combination of classical methods for sequence comparison and contig assembly, and of specifically written scripts and computer visualization routines. Comparisons were performed first against DNA and protein sequences from Saccharomyces cerevisiae, then against protein sequences from other completely sequenced organisms and, finally, against protein sequences from all other organisms. Blast alignments were individually inspected to help recognize genes within our random genomic sequences despite the fact that only parts of them were available. For each yeast species, validated alignments were used to infer the proper genetic code, to determine codon usage preferences and to calculate their degree of sequence divergence with S. cerevisiae. The quality of each genomic library was monitored from contig analysis of the DNA sequences. Annotated sequences were submitted to the EMBL database, and the general annotation tables produced served as a basis for our comparative description of the evolution, redundancy and function of the Hemiascomycete genomes described in other articles of this issue.
FEBS Letters | 2000
Claude Gaillardin; Guillemette Duchateau-Nguyen; Fredj Tekaia; Bertrand Llorente; Serge Casaregola; Claire Toffano-Nioche; Michel Aigle; François Artiguenave; Gaëlle Blandin; Monique Bolotin-Fukuhara; Elisabeth Bon; Jacky de Montigny; Bernard Dujon; Pascal Durrens; Andrée Lépingle; Alain Malpertuy; Cécile Neuvéglise; Odile Ozier-Kalogeropoulos; Serge Potier; William Saurin; Michel Termier; Micheline Wésolowski-Louvel; Patrick Wincker; Jean-Luc Souciet; Jean Weissenbach
We explored the biological diversity of hemiascomycetous yeasts using a set of 22 000 newly identified genes in 13 species through BLASTX searches. Genes without clear homologue in Saccharomyces cerevisiae appeared to be conserved in several species, suggesting that they were recently lost by S. cerevisiae. They often identified well‐known species‐specific traits. Cases of gene acquisition through horizontal transfer appeared to occur very rarely if at all. All identified genes were ascribed to functional classes. Functional classes were differently represented among species. Species classification by functional clustering roughly paralleled rDNA phylogeny. Unequal distribution of rapidly evolving, ascomycete‐specific, genes among species and functions was shown to contribute strongly to this clustering. A few cases of gene family amplification were documented, but no general correlation could be observed between functional differentiation of yeast species and variations of gene family sizes. Yeast biological diversity seems thus to result from limited species‐specific gene losses or duplications, and for a large part from rapid evolution of genes and regulatory factors dedicated to specific functions.