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Start Over Author "Kerrest A" Topic genome, fungal
3 results on '"Kerrest A"'

1. Comparative genomics of hemiascomycete yeasts: genes involved in DNA replication, repair, and recombination.

Author

Richard GF, Kerrest A, Lafontaine I, and Dujon B

Subjects
Amino Acid Sequence, Molecular Sequence Data, S Phase genetics, Sequence Homology, Amino Acid, Ascomycota genetics, DNA Repair genetics, DNA Replication, Genome, Fungal, Recombination, Genetic
Abstract

Among genes conserved from bacteria to mammals are those involved in replicating and repairing DNA. Following the complete sequencing of four hemiascomycetous yeast species during the course of the Genolevures 2 project, we have studied the conservation of 106 genes involved in replication, repair, and recombination in Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, and Yarrowia lipolytica and compared them with their Saccharomyces cerevisiae orthologues. We found that proteins belonging to the replication fork and to the nucleotide excision repair pathway were-on the average-more conserved than proteins involved in the checkpoint response to DNA damage or in meiotic recombination. The meiotic recombination proteins Spo11p and Mre11p-Rad50p, involved in making meiotic double-strand breaks (DSBs), are conserved as is Mus81p, involved in resolving meiotic recombination intermediates. Interestingly, genes found in organisms in which DSB-repair is required for proper synapsis during meiosis are also found in C. glabrata, K. lactis, and D. hansenii but not in Y. lipolytica, suggesting that two modes of meiotic recombination have been selected during evolution of the hemiascomycetous yeasts. In addition, we found that SGS1 and TOP1, respectively, a DEAD/DEAH helicase and a type I topoisomerase, are duplicated in C. glabrata and that SRS2, a helicase involved in homologous recombination, is tandemly duplicated in K. lactis. Phylogenetic analyses show that the duplicated SGS1 gene evolved faster than the original gene, probably leading to a specialization of function of the duplicated copy.

Published
2005
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2. Genome evolution in yeasts.

Author

Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, and Souciet JL

Subjects
Chromosomes, Fungal genetics, Conserved Sequence genetics, Gene Duplication, Molecular Sequence Data, RNA, Ribosomal genetics, RNA, Transfer genetics, Saccharomyces cerevisiae Proteins genetics, Synteny genetics, Tandem Repeat Sequences genetics, Evolution, Molecular, Genes, Fungal genetics, Genome, Fungal, Yeasts classification, Yeasts genetics
Abstract

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.

Published
2004
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3. Genome evolution in yeasts

Author

Valérie Barbe, Laurence Cattolico, Isabelle Lesur, Alix Kerrest, Hélène Ferry-Dumazet, Fabrice Confanioleri, Serge Casaregola, Emmanuel Talla, Véronique Anthouard, Jean-Marie Beckerich, Laurence Ma, Odile Ozier-Kalogeropoulos, Nicolas Jauniaux, Nicolas Goffard, Jacky de Montigny, David James Sherman, Antoine de Daruvar, Serge Potier, Guy-Franck Richard, Romain Koszul, Pascal Durrens, Anna Babour, Sophie Oztas, Emmanuelle Beyne, Christian Marck, Patrick Wincker, Emmanuelle Fabre, Stefan Pellenz, Bernard Dujon, Florence Hantraye, Eric Westhof, Cécile Fairhead, Micheline Wésolowski-Louvel, Cécile Neuvéglise, Gilles Fischer, Laurence Despons, Christophe Hennequin, Jean Weissenbach, Marie-Laure Straub, Audrey Suleau, Stéphanie Barnay, Jean-Marc Nicaud, Macha Nikolski, Claude Gaillardin, Claudine Bleykasten, Jean-Luc Souciet, Fredj Tekaia, Philippe Joyet, Rym Kachouri, Sylvie Blanchin, Bénédicte Wirth, Héloïse Muller, Christiane Bouchier, Maria Zeniou-Meyer, Ingrid Lafontaine, Jeanne Boyer, Monique Bolotin-Fukuhara, Ivan Zivanovic, Claude Scarpelli, Bernard Caudron, Agnès Thierry, Dominique Swennen, Alexis Groppi, Anita Boisramé, Michel Aigle, Lionel Frangeul, Marc Lemaire, Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Collection de Levures d'Intérêt Biotechnologique et Laboratoire de Génétique Moléculaire et Cellulaire, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Dynamique, évolution et expression de génomes de microorganismes (DEEGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Service de Biochimie, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génétique des Interactions Macromoléculaires, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Unité de Microbiologie et génétique (UMG), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Architecture et réactivité de l'ARN (ARN), Logiciels et Banques de Données, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Génomique (Plate-Forme), Institut Pasteur [Paris], Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
MESH: Tandem Re, MESH: Research Support, Non-U.S. Gov't, Genome, MESH: Saccharomyces cerevisiae Proteins, RNA, Transfer, Gene Duplication, Yeasts, Conserved Sequence, MESH: Evolution, Molecular, Segmental duplication, Genomic organization, Genetics, SACCHAROMYCES CEREVISIAE, 0303 health sciences, Multidisciplinary, MESH: Conserved Sequence, MESH: Yeasts, MESH: Gene Duplication, MESH: Synteny, Genome project, MESH: Chromosomes, Fungal, Tandem Repeat Sequences, MESH: Genome, Fungal, Chromosomes, Fungal, Genome, Fungal, GENETIC MAPPING, Genome evolution, Saccharomyces cerevisiae Proteins, Genes, Fungal, Molecular Sequence Data, Biology, Synteny, Evolution, Molecular, 03 medical and health sciences, GENOME ORGANIZATION, Molecular evolution, YEAST, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, 030304 developmental biology, Comparative genomics, STRUCTURE DU GENOME, MESH: Molecular Sequence Data, 030306 microbiology, MESH: RNA, Transfer, MOLECULAR EVOLUTION, MESH: Tandem Repeat Sequences, Evolutionary biology, RNA, Ribosomal, MESH: RNA, Ribosomal, MESH: Genes, Fungal
Abstract

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.

Published
2004
Full Text
View/download PDF

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