Amplification of a Zygosaccharomyces bailii DNA segment in wine yeast genomes by extrachromosomal circular DNA formation.

PubWeight™: 0.99‹?› | Rank: Top 15%

🔗 View Article (PMC 3053389)

Published in PLoS One on March 10, 2011

Authors

Virginie Galeote1, Frédéric Bigey, Emmanuelle Beyne, Maite Novo, Jean-Luc Legras, Serge Casaregola, Sylvie Dequin

Author Affiliations

1: INRA, UMR1083 Sciences Pour l'Œnologie, Montpellier, France.

Articles citing this

Evolutionary role of interspecies hybridization and genetic exchanges in yeasts. Microbiol Mol Biol Rev (2012) 1.11

Deciphering the hybridisation history leading to the Lager lineage based on the mosaic genomes of Saccharomyces bayanus strains NBRC1948 and CBS380. PLoS One (2011) 1.00

Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression. PLoS Genet (2013) 0.98

Differential adaptation to multi-stressed conditions of wine fermentation revealed by variations in yeast regulatory networks. BMC Genomics (2013) 0.93

Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production. Genome Biol Evol (2014) 0.89

Rapid evolution of recombinant Saccharomyces cerevisiae for Xylose fermentation through formation of extra-chromosomal circular DNA. PLoS Genet (2015) 0.88

The winemaker's bug: From ancient wisdom to opening new vistas with frontier yeast science. Bioeng Bugs (2012) 0.85

QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite. PLoS One (2014) 0.85

Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina). Genome Biol Evol (2013) 0.85

Genome Sequence of the Food Spoilage Yeast Zygosaccharomyces bailii CLIB 213T. Genome Announc (2013) 0.84

Lager yeast comes of age. Eukaryot Cell (2014) 0.83

Diversity and adaptive evolution of Saccharomyces wine yeast: a review. FEMS Yeast Res (2015) 0.81

Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts. Mol Biol Evol (2015) 0.81

Re-evaluation of glycerol utilization in Saccharomyces cerevisiae: characterization of an isolate that grows on glycerol without supporting supplements. Biotechnol Biofuels (2013) 0.80

Inferring Orthologs: Open Questions and Perspectives. Genomics Insights (2016) 0.79

Evolutionary mobility of the ribosomal DNA array in yeasts. Genome Biol Evol (2013) 0.78

Population structure and comparative genome hybridization of European flor yeast reveal a unique group of Saccharomyces cerevisiae strains with few gene duplications in their genome. PLoS One (2014) 0.76

Genetic Polymorphism in Wine Yeasts: Mechanisms and Methods for Its Detection. Front Microbiol (2017) 0.75

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol (1987) 266.90

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol (2007) 168.76

Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16

MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89

Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45

A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene (1987) 25.43

Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev (1999) 19.25

Yeast/E. coli shuttle vectors with multiple unique restriction sites. Yeast (1986) 17.88

Population genomics of domestic and wild yeasts. Nature (2009) 11.79

A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res (1996) 11.05

Genome evolution in yeasts. Nature (2004) 10.50

Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol (1996) 7.33

Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet (2000) 7.26

Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet (2008) 6.21

MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings. Trends Genet (2008) 6.00

Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol (1984) 5.39

Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harb Symp Quant Biol (1983) 4.85

Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature (2009) 3.67

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc Natl Acad Sci U S A (2007) 3.52

Yeast Mre11 and Rad1 proteins define a Ku-independent mechanism to repair double-strand breaks lacking overlapping end sequences. Mol Cell Biol (2003) 3.32

Nonhomologous end joining in yeast. Annu Rev Genet (2005) 3.32

Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics (2006) 2.70

Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history. Mol Ecol (2007) 2.70

Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms. Curr Biol (2006) 2.55

Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc Natl Acad Sci U S A (2009) 2.51

Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III. Mol Cell Biol (1990) 2.44

A catalog of neutral and deleterious polymorphism in yeast. PLoS Genet (2008) 2.28

Yeast evolutionary genomics. Nat Rev Genet (2010) 2.27

Patching broken chromosomes with extranuclear cellular DNA. Mol Cell (1999) 2.18

The amplification of ribosomal RNA genes involves a rolling circle intermediate. Proc Natl Acad Sci U S A (1973) 2.07

Mitochondrial DNA repairs double-strand breaks in yeast chromosomes. Nature (1999) 2.05

Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot Cell (2005) 1.95

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Res (2009) 1.94

Comparative genome analysis of a Saccharomyces cerevisiae wine strain. FEMS Yeast Res (2008) 1.76

Acquisition of prokaryotic genes by fungal genomes. Trends Genet (2009) 1.72

Analysis of the chromosomal DNA polymorphism of wine strains of Saccharomyces cerevisiae. Curr Genet (1992) 1.71

Molecular and functional organization of yeast plasmid pSR1. J Mol Biol (1985) 1.58

Formation of non-random extrachromosomal elements during development, differentiation and oncogenesis. Semin Cancer Biol (2006) 1.52

Functional and ecological impacts of horizontal gene transfer in eukaryotes. Curr Opin Genet Dev (2009) 1.42

Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser. BMC Genomics (2010) 1.33

Recent evolution of the human pathogen Cryptococcus neoformans by intervarietal transfer of a 14-gene fragment. Mol Biol Evol (2006) 1.32

Amplification of histone genes by circular chromosome formation in Saccharomyces cerevisiae. Nature (2006) 1.28

Identification of autonomously replicating circular subtelomeric Y' elements in Saccharomyces cerevisiae. Mol Cell Biol (1985) 1.21

Yeast plasmids resembling 2 micron DNA: regional similarities and diversities at the molecular level. J Bacteriol (1987) 1.17

Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus. Proc Natl Acad Sci U S A (2010) 1.10

Evolutionary capture of viral and plasmid DNA by yeast nuclear chromosomes. Eukaryot Cell (2009) 1.08

A multispecies-based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae. FEMS Yeast Res (2008) 1.04

Insertion of horizontally transferred genes within conserved syntenic regions of yeast genomes. PLoS One (2009) 1.04

Physical and functional structure of a yeast plasmid, pSB3, isolated from Zygosaccharomyces bisporus. Nucleic Acids Res (1985) 1.02

FSY1, a horizontally transferred gene in the Saccharomyces cerevisiae EC1118 wine yeast strain, encodes a high-affinity fructose/H+ symporter. Microbiology (2010) 1.00

Promiscuous DNA in the nuclear genomes of hemiascomycetous yeasts. FEMS Yeast Res (2008) 0.98

Plasmids resembling 2-micrometers DNA in the osmotolerant yeasts Saccharomyces bailii and Saccharomyces bisporus. J Gen Microbiol (1984) 0.96

A prominent role for segmental duplications in modeling eukaryotic genomes. C R Biol (2008) 0.95

A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes. ISME J (2011) 0.94

Formation of circular amplifications in Saccharomyces cerevisiae by a breakage-fusion-bridge mechanism. Environ Mol Mutagen (2000) 0.91

Formation of extrachromosomal circular DNA in HeLa cells by nonhomologous recombination. Nucleic Acids Res (1994) 0.85

Replication independent formation of extrachromosomal circular DNA in mammalian cell-free system. PLoS One (2009) 0.78

Articles by these authors

Genome evolution in yeasts. Nature (2004) 10.50

Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc Natl Acad Sci U S A (2009) 2.51

Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns. Nucleic Acids Res (2003) 2.21

Analysis of yeast populations during alcoholic fermentation: a six year follow-up study. Syst Appl Microbiol (2002) 1.39

Cofactor engineering in Saccharomyces cerevisiae: Expression of a H2O-forming NADH oxidase and impact on redox metabolism. Metab Eng (2006) 1.31

Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. Nucleic Acids Res (2006) 1.28

Effects of fermentation temperature and Saccharomyces species on the cell fatty acid composition and presence of volatile compounds in wine. Int J Food Microbiol (2003) 1.24

Functional analysis of the ALD gene family of Saccharomyces cerevisiae during anaerobic growth on glucose: the NADP+-dependent Ald6p and Ald5p isoforms play a major role in acetate formation. Microbiology (2004) 1.23

Bread, beer and wine: yeast domestication in the Saccharomyces sensu stricto complex. C R Biol (2011) 1.23

Deciphering the molecular basis of wine yeast fermentation traits using a combined genetic and genomic approach. G3 (Bethesda) (2011) 1.23

Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts. Nucleic Acids Res (2004) 1.22

A carotenoid cleavage dioxygenase from Vitis vinifera L.: functional characterization and expression during grape berry development in relation to C13-norisoprenoid accumulation. J Exp Bot (2005) 1.21

Engineering of 2,3-butanediol dehydrogenase to reduce acetoin formation by glycerol-overproducing, low-alcohol Saccharomyces cerevisiae. Appl Environ Microbiol (2009) 1.18

Role of social wasps in Saccharomyces cerevisiae ecology and evolution. Proc Natl Acad Sci U S A (2012) 1.17

Effect of fermentation temperature and culture media on the yeast lipid composition and wine volatile compounds. Int J Food Microbiol (2007) 1.16

Investigation by 13C-NMR and tricarboxylic acid (TCA) deletion mutant analysis of pathways for succinate formation in Saccharomyces cerevisiae during anaerobic fermentation. Microbiology (2003) 1.14

Control of ATP homeostasis during the respiro-fermentative transition in yeast. Mol Syst Biol (2010) 1.13

Effects of GPD1 overexpression in Saccharomyces cerevisiae commercial wine yeast strains lacking ALD6 genes. Appl Environ Microbiol (2006) 1.13

Food fermentations: microorganisms with technological beneficial use. Int J Food Microbiol (2011) 1.12

Phenotypic landscape of Saccharomyces cerevisiae during wine fermentation: evidence for origin-dependent metabolic traits. PLoS One (2011) 1.11

Genomic evolution of the long terminal repeat retrotransposons in hemiascomycetous yeasts. Genome Res (2002) 1.11

Characterization of natural hybrids of Saccharomyces cerevisiae and Saccharomyces bayanus var. uvarum. FEMS Yeast Res (2007) 1.03

A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation. BMC Genomics (2012) 1.03

Integration of transcriptomic and metabolic analyses for understanding the global responses of low-temperature winemaking fermentations. FEMS Yeast Res (2006) 1.03

Reduction of ethanol yield and improvement of glycerol formation by adaptive evolution of the wine yeast Saccharomyces cerevisiae under hyperosmotic conditions. Appl Environ Microbiol (2014) 1.02

Mutator-like element in the yeast Yarrowia lipolytica displays multiple alternative splicings. Eukaryot Cell (2005) 1.01

Sequential use of nitrogen compounds by Saccharomyces cerevisiae during wine fermentation: a model based on kinetic and regulation characteristics of nitrogen permeases. Appl Environ Microbiol (2012) 1.01

Ecological survey of Saccharomyces cerevisiae strains from vineyards in the Vinho Verde Region of Portugal. FEMS Microbiol Ecol (2005) 1.00

Deciphering the hybridisation history leading to the Lager lineage based on the mosaic genomes of Saccharomyces bayanus strains NBRC1948 and CBS380. PLoS One (2011) 1.00

FSY1, a horizontally transferred gene in the Saccharomyces cerevisiae EC1118 wine yeast strain, encodes a high-affinity fructose/H+ symporter. Microbiology (2010) 1.00

Survey of molecular methods for the typing of wine yeast strains. FEMS Microbiol Lett (2004) 0.99

Biodiversity of Saccharomyces yeast strains from grape berries of wine-producing areas using starter commercial yeasts. FEMS Yeast Res (2006) 0.99

Promiscuous DNA in the nuclear genomes of hemiascomycetous yeasts. FEMS Yeast Res (2008) 0.98

Evolutionary engineered Saccharomyces cerevisiae wine yeast strains with increased in vivo flux through the pentose phosphate pathway. Metab Eng (2011) 0.98

QTL mapping of the production of wine aroma compounds by yeast. BMC Genomics (2012) 0.97

Dissemination and survival of commercial wine yeast in the vineyard: a large-scale, three-years study. FEMS Yeast Res (2005) 0.96

Delimitation of the species of the Debaryomyces hansenii complex by intron sequence analysis. Int J Syst Evol Microbiol (2009) 0.95

A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis (2006) 0.95

Nitrogen catabolite repression in Saccharomyces cerevisiae during wine fermentations. FEMS Yeast Res (2004) 0.94

A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes. ISME J (2011) 0.94

Yeast ecology in French cider and black olive natural fermentations. Int J Food Microbiol (2005) 0.94

Genetic characterization of commercial Saccharomyces cerevisiae isolates recovered from vineyard environments. Yeast (2007) 0.94

Differential adaptation to multi-stressed conditions of wine fermentation revealed by variations in yeast regulatory networks. BMC Genomics (2013) 0.93

Reversal of coenzyme specificity of 2,3-butanediol dehydrogenase from Saccharomyces cerevisae and in vivo functional analysis. Biotechnol Bioeng (2009) 0.93

Role in anaerobiosis of the isoenzymes for Saccharomyces cerevisiae fumarate reductase encoded by OSM1 and FRDS1. Yeast (2007) 0.93

Genetic analysis of geraniol metabolism during fermentation. Food Microbiol (2012) 0.93

Biodiversity in sulfur metabolism in hemiascomycetous yeasts. FEMS Yeast Res (2011) 0.91

A constraint-based model analysis of the metabolic consequences of increased NADPH oxidation in Saccharomyces cerevisiae. Metab Eng (2012) 0.91

Role of Saccharomyces cerevisiae oxidoreductases Bdh1p and Ara1p in the metabolism of acetoin and 2,3-butanediol. Appl Environ Microbiol (2009) 0.90

The lipase/acyltransferase from Candida parapsilosis: molecular cloning and characterization of purified recombinant enzymes. Eur J Biochem (2002) 0.88

Safety assessment of dairy microorganisms: the hemiascomycetous yeasts. Int J Food Microbiol (2007) 0.88

Gene expression and biochemical analysis of cheese-ripening yeasts: focus on catabolism of L-methionine, lactate, and lactose. Appl Environ Microbiol (2007) 0.88

Engineering a Saccharomyces cerevisiae wine yeast that exhibits reduced ethanol production during fermentation under controlled microoxygenation conditions. Appl Environ Microbiol (2006) 0.87

Kluyveromyces lactis and Saccharomyces cerevisiae, two potent deacidifying and volatile-sulphur-aroma-producing microorganisms of the cheese ecosystem. Appl Microbiol Biotechnol (2006) 0.85

Sfl1p acts as an activator of the HSP30 gene in Saccharomyces cerevisiae. Curr Genet (2007) 0.85

Genome Sequence of the Food Spoilage Yeast Zygosaccharomyces bailii CLIB 213T. Genome Announc (2013) 0.84

Glycogen synthesis in the absence of glycogenin in the yeast Saccharomyces cerevisiae. FEBS Lett (2005) 0.84

High-level expression of Candida parapsilosis lipase/acyltransferase in Pichia pastoris. J Biotechnol (2004) 0.84

Identification of yeasts during alcoholic fermentation of tchapalo, a traditional sorghum beer from Côte d'Ivoire. Antonie Van Leeuwenhoek (2011) 0.84

A novel lipase/acyltransferase from the yeast Candida albicans: expression and characterisation of the recombinant enzyme. Appl Microbiol Biotechnol (2005) 0.84

YeastIP: a database for identification and phylogeny of Saccharomycotina yeasts. FEMS Yeast Res (2012) 0.83

The genomes of fermentative Saccharomyces. C R Biol (2011) 0.83

Production of a recombinant carotenoid cleavage dioxygenase from grape and enzyme assay in water-miscible organic solvents. Biotechnol Lett (2007) 0.82

Pilot-scale evaluation the enological traits of a novel, aromatic wine yeast strain obtained by adaptive evolution. Food Microbiol (2012) 0.82

L-methionine degradation pathway in Kluyveromyces lactis: identification and functional analysis of the genes encoding L-methionine aminotransferase. Appl Environ Microbiol (2006) 0.82

New insights into {gamma}-aminobutyric acid catabolism: Evidence for {gamma}-hydroxybutyric acid and polyhydroxybutyrate synthesis in Saccharomyces cerevisiae. Appl Environ Microbiol (2009) 0.82

The Kluyveromyces lactis repertoire of transcriptional regulators. FEMS Yeast Res (2006) 0.82

Glucose utilization of strains lacking PGI1 and expressing a transhydrogenase suggests differences in the pentose phosphate capacity among Saccharomyces cerevisiae strains. FEMS Yeast Res (2007) 0.82

Effect of organic acids and nitrogen source on alcoholic fermentation: study of their buffering capacity. J Agric Food Chem (2003) 0.81

Combined effects of nutrients and temperature on the production of fermentative aromas by Saccharomyces cerevisiae during wine fermentation. Appl Microbiol Biotechnol (2014) 0.81

Transcriptomic analysis of extensive changes in metabolic regulation in Kluyveromyces lactis strains. Eukaryot Cell (2006) 0.81

Computational models for prediction of yeast strain potential for winemaking from phenotypic profiles. PLoS One (2013) 0.80

Insights into the life cycle of yeasts from the CTG clade revealed by the analysis of the Millerozyma (Pichia) farinosa species complex. PLoS One (2012) 0.80

A genetic approach of wine yeast fermentation capacity in nitrogen-starvation reveals the key role of nitrogen signaling. BMC Genomics (2014) 0.80

Novel transporters from hemiascomycete yeasts. J Mol Microbiol Biotechnol (2003) 0.79

The Saccharomyces cerevisiae zinc factor protein Stb5p is required as a basal regulator of the pentose phosphate pathway. FEMS Yeast Res (2010) 0.79

Population polymorphism of nuclear mitochondrial DNA insertions reveals widespread diploidy associated with loss of heterozygosity in Debaryomyces hansenii. Eukaryot Cell (2010) 0.79

Efficient ammonium uptake and mobilization of vacuolar arginine by Saccharomyces cerevisiae wine strains during wine fermentation. Microb Cell Fact (2014) 0.78

Intraspecific gene expression variability in the yeast Kluyveromyces lactis revealed by micro-array analysis. FEMS Yeast Res (2005) 0.78

An impaired ubiquitin ligase complex favors initial growth of auxotrophic yeast strains in synthetic grape must. Appl Microbiol Biotechnol (2014) 0.78

Stuck fermentation: development of a synthetic stuck wine and study of a restart procedure. Int J Food Microbiol (2013) 0.77

De novo transcriptomic resources for two sibling species of moths: Ostrinia nubilalis and O. scapulalis. BMC Res Notes (2013) 0.77

French Jura flor yeasts: genotype and technological diversity. Antonie Van Leeuwenhoek (2009) 0.77

Overexpression and characterization of two human salivary proline rich proteins. Protein Expr Purif (2006) 0.76

Novel starters for old processes: use of Saccharomyces cerevisiae strains isolated from artisanal sourdough for craft beer production at a brewery scale. J Ind Microbiol Biotechnol (2014) 0.75

Erratum: Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle. Sci Rep (2017) 0.75

Increased diversity in the genus Debaryomyces from Arctic glacier samples. Antonie Van Leeuwenhoek (2014) 0.75

Corrigendum: Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Sci Rep (2015) 0.75