Author Report for: Casaregola SNo contact information in database for Casaregola S
Louis VL, Despons L, Friedrich A, Martin T, Durrens P, Casaregola S, Neuveglise C, Fairhead C, Marck C and Souciet JL <33 more author(s)> Louis VL, Despons L, Friedrich A, Martin T, Durrens P, Casaregola S, Neuveglise C, Fairhead C, Marck C, Cruz JA, Straub ML, Kugler V, Sacerdot C, Uzunov Z, Thierry A, Weiss S, Bleykasten C, De Montigny J, Jacques N, Jung P, Lemaire M, Mallet S, Morel G, Richard GF, Sarkar A, Savel G, Schacherer J, Seret ML, Talla E, Samson G, Jubin C, Poulain J, Vacherie B, Barbe V, Pelletier E, Sherman DJ, Westhof E, Weissenbach J, Baret PV, Wincker P, Gaillardin C, Dujon B, Souciet JL (- 33) Ref: G3 (Bethesda), 2:299, 2012 : PubMed ESTHER: Louis_2012_G3.(Bethesda)_2_299 PubMedSearch: Louis 2012 G3.(Bethesda) 2 299 PubMedID: 22384408 Gene_locus related to this paper: picso-g8ycc9, picso-g8yet0, picso-g8yb96, picso-g8ym39, erecy-g8jrp5, picso-g8y652 Abstract Polyploidization is an important process in the evolution of eukaryotic genomes, but ensuing molecular mechanisms remain to be clarified. Autopolyploidization or whole-genome duplication events frequently are resolved in resulting lineages by the loss of single genes from most duplicated pairs, causing transient gene dosage imbalance and accelerating speciation through meiotic infertility. Allopolyploidization or formation of interspecies hybrids raises the problem of genetic incompatibility (Bateson-Dobzhansky-Muller effect) and may be resolved by the accumulation of mutational changes in resulting lineages. In this article, we show that an osmotolerant yeast species, Pichia sorbitophila, recently isolated in a concentrated sorbitol solution in industry, illustrates this last situation. Its genome is a mosaic of homologous and homeologous chromosomes, or parts thereof, that corresponds to a recently formed hybrid in the process of evolution. The respective parental contributions to this genome were characterized using existing variations in GC content. The genomic changes that occurred during the short period since hybrid formation were identified (e.g., loss of heterozygosity, unilateral loss of rDNA, reciprocal exchange) and distinguished from those undergone by the two parental genomes after separation from their common ancestor (i.e., NUMT (NUclear sequences of MiTochondrial origin) insertions, gene acquisitions, gene location movements, reciprocal translocation). We found that the physiological characteristics of this new yeast species are determined by specific but unequal contributions of its two parents, one of which could be identified as very closely related to an extant Pichia farinosa strain. Title: Complete genome sequence of the probiotic Lactobacillus casei strain BL23 Maze A, Boel G, Zuniga M, Bourand A, Loux V, Yebra MJ, Monedero V, Correia K, Jacques N and Deutscher J <11 more author(s)> Maze A, Boel G, Zuniga M, Bourand A, Loux V, Yebra MJ, Monedero V, Correia K, Jacques N, Beaufils S, Poncet S, Joyet P, Milohanic E, Casaregola S, Auffray Y, Perez-Martinez G, Gibrat JF, Zagorec M, Francke C, Hartke A, Deutscher J (- 11) Ref: Journal of Bacteriology, 192:2647, 2010 : PubMed ESTHER: Maze_2010_J.Bacteriol_192_2647 PubMedSearch: Maze 2010 J.Bacteriol 192 2647 PubMedID: 20348264 Gene_locus related to this paper: lacc3-q03b36, lacc3-q036j3, lacca-q6edz1, laccb-b3w942, laccb-b3wcx2, lacrh-pepr Abstract The entire genome of Lactobacillus casei BL23, a strain with probiotic properties, has been sequenced. The genomes of BL23 and the industrially used probiotic strain Shirota YIT 9029 (Yakult) seem to be very similar. Title: Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118 Novo M, Bigey F, Beyne E, Galeote V, Gavory F, Mallet S, Cambon B, Legras JL, Wincker P and Dequin S <1 more author(s)> Novo M, Bigey F, Beyne E, Galeote V, Gavory F, Mallet S, Cambon B, Legras JL, Wincker P, Casaregola S, Dequin S (- 1) Ref: Proc Natl Acad Sci U S A, 106:16333, 2009 : PubMed ESTHER: Novo_2009_Proc.Natl.Acad.Sci.U.S.A_106_16333 PubMedSearch: Novo 2009 Proc.Natl.Acad.Sci.U.S.A 106 16333 PubMedID: 19805302 Gene_locus related to this paper: yeast-AIM2, yeast-BST1, yeast-cbpy1, yeast-cld1, yeast-dap1, yeast-dap2, yeast-dlhh, yeast-ECM18, yeast-FSH1, yeast-FSH3, yeast-ict1, yeast-kex01, yeast-MCFS1, yeast-MCFS2, yeast-met2, yeast-mgll, yeast-pdat, yeast-ppme1, yeast-ROG1, yeast-SAY1, yeast-tgl1, yeast-tgl2, yeast-yby9, yeast-YDL109C, yeast-YDR428C, yeast-YDR444W, yeast-yg19, yeast-yj77, yeast-yjg8, yeast-YLL012W, yeast-YLR020C, yeast-YLR118c, yeast-ym60, yeast-ynl5, yeast-yo059, yeast-YPR147C, yeast-hda1 Abstract Saccharomyces cerevisiae has been used for millennia in winemaking, but little is known about the selective forces acting on the wine yeast genome. We sequenced the complete genome of the diploid commercial wine yeast EC1118, resulting in an assembly of 31 scaffolds covering 97% of the S288c reference genome. The wine yeast differed strikingly from the other S. cerevisiae isolates in possessing 3 unique large regions, 2 of which were subtelomeric, the other being inserted within an EC1118 chromosome. These regions encompass 34 genes involved in key wine fermentation functions. Phylogeny and synteny analyses showed that 1 of these regions originated from a species closely related to the Saccharomyces genus, whereas the 2 other regions were of non-Saccharomyces origin. We identified Zygosaccharomyces bailii, a major contaminant of wine fermentations, as the donor species for 1 of these 2 regions. Although natural hybridization between Saccharomyces strains has been described, this report provides evidence that gene transfer may occur between Saccharomyces and non-Saccharomyces species. We show that the regions identified are frequent and differentially distributed among S. cerevisiae clades, being found almost exclusively in wine strains, suggesting acquisition through recent transfer events. Overall, these data show that the wine yeast genome is subject to constant remodeling through the contribution of exogenous genes. Our results suggest that these processes are favored by ecologic proximity and are involved in the molecular adaptation of wine yeasts to conditions of high sugar, low nitrogen, and high ethanol concentrations. Title: Comparative genomics of protoploid Saccharomycetaceae Souciet JL, Dujon B, Gaillardin C, Johnston M, Baret PV, Cliften P, Sherman DJ, Weissenbach J, Westhof E and Talla E <44 more author(s)> Souciet JL, Dujon B, Gaillardin C, Johnston M, Baret PV, Cliften P, Sherman DJ, Weissenbach J, Westhof E, Wincker P, Jubin C, Poulain J, Barbe V, Segurens B, Artiguenave F, Anthouard V, Vacherie B, Val ME, Fulton RS, Minx P, Wilson R, Durrens P, Jean G, Marck C, Martin T, Nikolski M, Rolland T, Seret ML, Casaregola S, Despons L, Fairhead C, Fischer G, Lafontaine I, Leh V, Lemaire M, De Montigny J, Neuveglise C, Thierry A, Blanc-Lenfle I, Bleykasten C, Diffels J, Fritsch E, Frangeul L, Goeffon A, Jauniaux N, Kachouri-Lafond R, Payen C, Potier S, Pribylova L, Ozanne C, Richard GF, Sacerdot C, Straub ML, Talla E (- 44) Ref: Genome Res, 19:1696, 2009 : PubMed ESTHER: Souciet_2009_Genome.Res_19_1696 PubMedSearch: Souciet 2009 Genome.Res 19 1696 PubMedID: 19525356 Gene_locus related to this paper: lactc-c5dci9, lactc-c5ddi5, lactc-c5dew5, lactc-c5dez1, lactc-c5df11, lactc-c5dfh7, lactc-c5dgd1, lactc-c5dif7, lactc-c5din7, lactc-c5dja0, lactc-c5dm95, lactc-c5dn06, lactc-c5dnn9, lactc-c5e2g8, lactc-c5e3n5, lactc-c5e375, zygrc-c5drr0, zygrc-c5dvh0, zygrc-c5dvl2, zygrc-c5dvx0, zygrc-c5dvz8, zygrc-c5dx83, zygrc-c5dxn5, zygrc-c5dxq9, zygrc-c5e0w1, zygrc-c5e1e4, zygrc-c5e1h2, zygro-a0a1q2zt01, 9sach-a0a0p1kuu1, lactc-kex1, zygrc-kex1 Abstract Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified. Title: Identification and characterisation of LIP7 and LIP8 genes encoding two extracellular triacylglycerol lipases in the yeast Yarrowia lipolytica Fickers P, Fudalej F, Le Dall MT, Casaregola S, Gaillardin C, Thonart P, Nicaud JM Ref: Fungal Genet Biol, 42:264, 2005 : PubMed ESTHER: Fickers_2005_Fungal.Genet.Biol_42_264 PubMedSearch: Fickers 2005 Fungal.Genet.Biol 42 264 PubMedID: 15707847 Gene_locus related to this paper: yarli-LIP7, yarli-LIP8 Abstract In the lipolytic yeast Yarrowia lipolytica, the LIP2 gene was previously reported to encode an extracellular lipase. The growth of a Deltalip2 strain on triglycerides as sole carbon source suggest an alternative pathway for triglycerides utilisation in this yeast. Here, we describe the isolation and the characterisation of the LIP7 and LIP8 genes which were found to encode a 366 and a 371-amino acid precursor protein, respectively. These proteins which belong to the triacylglycerol hydrolase family (EC 3.1.1.3) presented a high homology with the extracellular lipase CdLIP2 and CdLIP3 from Candida deformans. The physiological function of the lipase isoenzymes was investigated by creating single and multi-disrupted strains. Lip7p and Lip8p were found to correspond to active secreted lipases. The lack of lipase production in a Deltalip2 Deltalip7 Deltalip8 strain suggest that no additional extracellular lipase remains to be discovered in Y. lipolytica. The substrate specificity towards synthetic ester molecules indicates that Lip7p presented a maximum activity centred on caproate (C6) while that of Lip8p is in caprate (C10). Title: Genome evolution in yeasts Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuveglise C and Souciet JL <57 more author(s)> Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuveglise 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, Boisrame 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, Wesolowski-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, Souciet JL (- 57) Ref: Nature, 430:35, 2004 : PubMed ESTHER: Dujon_2004_Nature_430_35 PubMedSearch: Dujon 2004 Nature 430 35 PubMedID: 15229592 Gene_locus related to this paper: canga-apth1, canga-ppme1, canga-q6fik7, canga-q6fiv5, canga-q6fiw8, canga-q6fj11, canga-q6fjh6, canga-q6fjl0, canga-q6fjr8, canga-q6fkj6, canga-q6fkm9, canga-q6fku7, canga-q6fl14, canga-q6flb5, canga-q6fle9, canga-q6flk8, canga-q6fly1, canga-q6fly9, canga-q6fmz4, canga-q6fnx4, canga-q6fp28, canga-q6fpa8, canga-q6fpi6, canga-q6fpv7, canga-q6fpw6, canga-q6fqj3, canga-q6fr97, canga-q6frt7, canga-q6ftm9, canga-q6ftu0, canga-q6ftv9, canga-q6ftz9, canga-q6fuf8, canga-q6fv41, canga-q6fvu3, canga-q6fw36, canga-q6fw94, canga-q6fwk6, canga-q6fwm0, canga-q6fxc7, canga-q6fxd7, debha-apth1, debha-atg15, debha-b5rtk1, debha-b5rub4, debha-b5rue8, debha-b5rue9, debha-bna7, debha-ppme1, debha-q6bgx3, debha-q6bh69, debha-q6bhb8, debha-q6bhc1, debha-q6bhd0, debha-q6bhj7, debha-q6bi97, debha-q6biq7, debha-q6bj53, debha-q6bkd8, debha-q6bks1, debha-q6bky4, debha-q6bm63, debha-q6bmh3, debha-q6bn89, debha-q6bnj6, debha-q6bp08, debha-q6bpb4, debha-q6bpc0, debha-q6bpc6, debha-q6bq10, debha-q6bq11, debha-q6bqd9, debha-q6bqj6, debha-q6br33, debha-q6br93, debha-q6brg1, debha-q6brw7, debha-q6bs23, debha-q6bsc3, debha-q6bsl8, debha-q6bsx6, debha-q6bta5, debha-q6bty5, debha-q6btz0, debha-q6bu73, debha-q6buk9, debha-q6but7, debha-q6bvc4, debha-q6bvg4, debha-q6bvg8, debha-q6bvp4, debha-q6bw82, debha-q6bxr7, debha-q6bxu9, debha-q6bym5, debha-q6byn7, debha-q6bzj8, debha-q6bzk2, debha-q6bzm5, klula-apth1, klula-ppme1, klula-q6cin9, klula-q6ciu6, klula-q6cj47, klula-q6cjc8, klula-q6cjq9, klula-q6cjs1, klula-q6cjv9, klula-q6ckd7, klula-q6ckk4, klula-q6ckx4, klula-q6cl20, klula-q6clm1, klula-q6cly8, klula-q6clz7, klula-q6cm48, klula-q6cm49, klula-q6cmt5, klula-q6cn71, klula-q6cnm1, klula-q6cr74, klula-q6cr90, klula-q6crs0, klula-q6crv8, klula-q6crz9, klula-q6cst8, klula-q6csv8, klula-q6ctp8, klula-q6cu02, klula-q6cu78, klula-q6cu79, klula-q6cuv3, klula-q6cvd3, klula-q6cw70, klula-q6cw92, klula-q6cwu7, klula-q6cx84, klula-q6cxa3, klula-q6cy41, yarli-apth1, yarli-atg15, yarli-BST1B, yarli-lip2, yarli-LIP3, yarli-LIP4, yarli-LIP5, yarli-LIP7, yarli-LIP8, yarli-lipa1, yarli-ppme1, yarli-q6bzp1, yarli-q6bzv7, yarli-q6c1f5, yarli-q6c1f7, yarli-q6c1r3, yarli-q6c2z2, yarli-q6c3h1, yarli-q6c3i6, yarli-q6c3l1, yarli-q6c3u6, yarli-q6c4h8, yarli-q6c5j1, yarli-q6c5m4, yarli-q6c6m4, yarli-q6c6p7, yarli-q6c6v2, yarli-q6c7h3, yarli-q6c7i7, yarli-q6c7j5, yarli-q6c7y6, yarli-q6c8m4, yarli-q6c8q4, yarli-q6c8u4, yarli-q6c8y2, yarli-q6c9r0, yarli-q6c9r1, yarli-q6c9u0, yarli-q6c9v4, yarli-q6c209, yarli-q6c225, yarli-q6c493, yarli-q6c598, yarli-q6c687, yarli-q6c822, yarli-q6cau6, yarli-q6cax2, yarli-q6caz1, yarli-q6cb63, yarli-q6cba7, yarli-q6cbb1, yarli-q6cbe6, yarli-q6cby1, yarli-q6ccr0, yarli-q6cdg1, yarli-q6cdi6, yarli-q6cdv9, yarli-q6ce37, yarli-q6ceg0, yarli-q6cep3, yarli-q6cey5, yarli-q6cf60, yarli-q6cfp3, yarli-q6cfx2, yarli-q6cg13, yarli-q6cg27, yarli-q6cgj3, yarli-q6chb8, yarli-q6ci59, yarli-q6c748, canga-q6fpj0, klula-q6cp11, yarli-q6c4p0, debha-q6btp5, debha-kex1 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. Title: Analysis of the constitution of the beer yeast genome by PCR, sequencing and subtelomeric sequence hybridization Casaregola S, Nguyen HV, Lapathitis G, Kotyk A, Gaillardin C Ref: Int J Syst Evol Microbiol, 51:1607, 2001 : PubMed ESTHER: Casaregola_2001_Int.J.Syst.Evol.Microbiol_51_1607 PubMedSearch: Casaregola 2001 Int.J.Syst.Evol.Microbiol 51 1607 PubMedID: 11491364 Gene_locus related to this paper: yeast-met2 Abstract The lager brewing yeasts, Saccharomyces pastorianus (synonym Saccharomyces carlsbergensis), are allopolyploid, containing parts of two divergent genomes. Saccharomyces cerevisiae contributed to the formation of these hybrids, although the identity of the other species is still unclear. The presence of alleles specific to S. cerevisiae and S. pastorianus was tested for by PCR/RFLP in brewing yeasts of various origins and in members of the Saccharomyces sensu stricto complex. S. cerevisiae-type alleles of two genes, HIS4 and YCL008c, were identified in another brewing yeast, S. pastorianus CBS 1503 (Saccharomyces monacensis), thought to be the source of the other contributor to the lager hybrid. This is consistent with the hybridization of S. cerevisiae subtelomeric sequences X and Y' to the electrophoretic karyotype of this strain. S. pastorianus CBS 1503 (S. monacensis) is therefore probably not an ancestor of S. pastorianus, but a related hybrid. Saccharomyces bayanus, also thought to be one of the contributors to the lager yeast hybrid, is a heterogeneous taxon containing at least two subgroups, one close to the type strain, CBS 380T, the other close to CBS 395 (Saccharomyces uvarum). The partial sequences of several genes (HIS4, MET10, URA3) were shown to be identical or very similar (over 99%) in S. pastorianus CBS 1513 (S. carlsbergensis), S. bayanus CBS 380T and its close derivatives, showing that S. pastorianus and S. bayanus have a common ancestor. A distinction between two subgroups within S. bayanus was made on the basis of sequence analysis: the subgroup represented by S. bayanus CBS 395 (S. uvarum) has 6-8% sequence divergence within the genes HIS4, MET10 and MET2 from S. bayanus CBS 380T, indicating that the two S. bayanus subgroups diverged recently. The detection of specific alleles by PCR/RFLP and hybridization with S. cerevisiae subtelomeric sequences X and Y' to electrophoretic karyotypes of brewing yeasts and related species confirmed our findings and revealed substantial heterogeneity in the genome constitution of Czech brewing yeasts used in production. | |||||||
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