Claire Toffano-Nioche
University of Paris
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Featured researches published by Claire Toffano-Nioche.
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’.
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.
Plant Physiology | 2006
Eric Rivals; Clémence Bruyère; Claire Toffano-Nioche; Alain Lecharny
In Arabidopsis (Arabidopsis thaliana) the 466 pentatricopeptide repeat (PPR) proteins are putative RNA-binding proteins with essential roles in organelles. Roughly half of the PPR proteins form the plant combinatorial and modular protein (PCMP) subfamily, which is land-plant specific. PCMPs exhibit a large and variable tandem repeat of a standard pattern of three PPR variant motifs. The association or not of this repeat with three non-PPR motifs at their C terminus defines four distinct classes of PCMPs. The highly structured arrangement of these motifs and the similar repartition of these arrangements in the four classes suggest precise relationships between motif organization and substrate specificity. This study is an attempt to reconstruct an evolutionary scenario of the PCMP family. We developed an innovative approach based on comparisons of the proteins at two levels: namely the succession of motifs along the protein and the amino acid sequence of the motifs. It enabled us to infer evolutionary relationships between proteins as well as between the inter- and intraprotein repeats. First, we observed a polarized elongation of the repeat from the C terminus toward the N-terminal region, suggesting local recombinations of motifs. Second, the most N-terminal PPR triple motif proved to evolve under different constraints than the remaining repeat. Altogether, the evidence indicates different evolution for the PPR region and the C-terminal one in PCMPs, which points to distinct functions for these regions. Moreover, local sequence homogeneity observed across PCMP classes may be due to interclass shuffling of motifs, or to deletions/insertions of non-PPR motifs at the C terminus.
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
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.
Genome Research | 2001
Nathalie Boudet; Sébastien Aubourg; Claire Toffano-Nioche; Martin Kreis; Alain Lecharny
Plant Biotechnology Journal | 2004
Annaïck Mingam; Claire Toffano-Nioche; Véronique Brunaud; Nathalie Boudet; Martin Kreis; Alain Lecharny