[method for producing spheroplasts from yeast cells].a method for producing spheroplasts from yeast cells has been developed. the method involves: 1) prefreezing and thawing of cells in the minimal nutrient medium; 2) treatment with the mixture of 86 mm 2-mercaptoethanol, 5% sodium dodecylsulphate and 6% triton x-100; 3) enzymic digestion by the digestive juice of grape helix. the formation of spheroplasts was controlled by microscopy and measurement of the optic density of the spheroplast suspension in the incubation medium and in 1% sodium dodec ...19751107988
genetic identification of natural saccharomyces sensu stricto yeasts from finland, holland and slovakia.genetic and karyotypic studies of natural saccharomyces sensu stricto yeasts from finland, holland and slovakia revealed three wild sibling-species: saccharomyces cerevisiae, saccharomyces bayanus and saccharomyces paradoxus.19921519919
[comparative genetics of yeasts. xxiii. unusual inheritance of toxin formation in saccharomyces paradoxus batschinskaia].the data about cytoplasmic control of toxin formation in saccharomyces paradoxus cbs5829 are presented. a novel determinant (kil-k3) is probably located in the mitochondrial genome. in other mutations, adenine deficiency results in suppression of toxin formation of the k3 type. a new killer plasmid (kil-kx) was detected in sacch. paradoxus vkm y-2472.19854076767
temperature sensitive radiosensitive mutants of the yeast saccharomyces paradoxus. 19734777792
[genetic control of sporulation in saccharomyces paradoxus yeasts]. 19734807112
the saccharomyces ty5 retrotransposon family is associated with origins of dna replication at the telomeres and the silent mating locus hmr.we have characterized the genomic organization of the ty5 retrotransposons among diverse strains of saccharomyces cerevisiae and the related species saccharomyces paradoxus. the s. cerevisiae strain s288c (or its derivatives) carries eight ty5 insertions. six of these are located near the telomeres, and five are found within 500 bp of autonomously replicating sequences present in the type x subtelomeric repeat. the remaining two s. cerevisiae elements are adjacent to the silent mating locus hmr ...19957846079
electrophoretic karyotypes of authentic strains of the sensu stricto group of the genus saccharomyces.a comparative electrophoretic karyotyping study was performed with several certified authentic strains of the four species that could be distinguished by nuclear dna (ndna)-ndna reassociation data within the sensu stricto group of the genus saccharomyces. a multivariate analysis of the polymorphisms observed in pulsed-field gel electrophoretic profiles (numbers and molecular weights of separated units) revealed that the strains could be separated into four clusters that corresponded to the taxa ...19947981105
the chromosome end in yeast: its mosaic nature and influence on recombinational dynamics.yeast chromosome ends are composed of several different repeated elements. among six clones of chromosome ends from two strains of saccharomyces cerevisiae, at least seven different repeated sequence families were found. these included the previously identified y' and x elements. some families are highly variable in copy number and location between strains of s. cerevisiae, while other elements appear constant in copy number and location. three repeated sequence elements are specific to s. cerev ...19948005434
genetic variation of the repeated mal loci in natural populations of saccharomyces cerevisiae and saccharomyces saccharomyces cerevisiae, the gene functions required to ferment the disaccharide maltose are encoded by the mal loci. any one of five highly sequence homologous mal loci identified in various s. cerevisiae strains (called mal1, 2, 3, 4 and 6) is sufficient to ferment maltose. each is a complex of three genes encoding maltose permease, maltase and a transcription activator. this family of loci maps to telomere-linked positions on different chromosomes and most natural strains contain more tha ...19948005435
the mismatch repair system contributes to meiotic sterility in an interspecific yeast hybrid.the mismatch repair system is the major barrier to genetic recombination during interspecific sexual conjugation in prokaryotes. the existence of this anti-recombination activity has implications for theories of evolution and the isolation of species. to determine if this phenomenon occurs in eukaryotes, the effect of a deficiency of mismatch repair on the meiotic sterility of an interspecific hybrid of saccharomyces cerevisiae and the closely related species saccharomyces paradoxus was examined ...19968612597
the mismatch repair system reduces meiotic homeologous recombination and stimulates recombination-dependent chromosome loss.efficient genetic recombination requires near-perfect homology between participating molecules. sequence divergence reduces the frequency of recombination, a process that is dependent on the activity of the mismatch repair system. the effects of chromosomal divergence in diploids of saccharomyces cerevisiae in which one copy of chromosome iii is derived from a closely related species, saccharomyces paradoxus, have been examined. meiotic recombination between the diverged chromosomes is decreased ...19968887641
differentiation of european and far east asian populations of saccharomyces paradoxus by allozyme analysis.allozyme electrophoresis was used to characterize 39 isolates belonging to the wild yeast species saccharomyces paradoxus for variation at nine enzyme loci. the data revealed significant genetic differentiation between isolates from two geographically distinct regions, one including continental europe and the other including the russian far east and japan. the results are consistent with previous observations indicating that there is partial reproductive isolation between isolates collected from ...19979103619
a phylogenetic analysis of the genus saccharomyces based on 18s rrna gene sequences: description of saccharomyces kunashirensis sp. nov. and saccharomyces martiniae sp. nov.a phylogenetic investigation of the ascomycetous yeast genus saccharomyces was performed by using 18s rrna gene sequence analysis. comparative sequence analysis showed that the genus is phylogenetically very heterogeneous. saccharomyces species were found to be phylogenetically interdispersed with members of other ascomycetous genera (e.g., the genera kluyveromyces, torulaspora, and zygosaccharomyces). the four species of the saccharomyces sensu stricto complex (viz., saccharomyces bayanus, sacc ...19979103636
phylogenetic analysis of the saccharomyces cerevisiae group based on polymorphisms of rdna spacer sequences.the phylogenetic relationships between species of yeasts assigned to the saccharomyces sensu stricto group, which includes saccharomyces cerevisiae and saccharomyces bayanus, were studied together with saccharomyces pastorianus and saccharomyces paradoxus. the experimental approaches used were rflp analysis of the pcr-amplified rdna internal transcribed spacer (its) and intergenic spacer, and total its sequence analysis. both rflp and sequence analyses gave fairly similar results. the gene trees ...19989542100
saccharomyces paradoxus and saccharomyces cerevisiae are associated with exudates of north american oaks.genetic hybridization and karyotypic analyses revealed the biological species saccharomyces paradoxus and saccharomyces cerevisiae in exudates from north american oaks for the first time. in addition, two strains collected from elm flux and from drosophila by phaff in 1961 and 1952 were reidentified as s. paradoxus. each strain studied showed a unique profile of chromosomal hybridization with a probe for the retrotransposable element ty1. the wild distribution of natural saccharomyces sensu stri ...199810029999
[divergent populations od saccharomyces paradoxus in hawaii: species in statu nascendi]. 199910188089
distinctive electrophoretic isoenzyme profiles in saccharomyces sensu stricto.genetic variation among 35 strains representing the four currently recognized species of saccharomyces sensu stricto (saccharomyces cerevisiae, saccharomyces bayanus, saccharomyces pastorianus/carlsbergensis and saccharomyces paradoxus) was estimated by analysing the electrophoretic mobilities of nonspecific esterases, acid phosphatase, lactate dehydrogenase and glucose-6-phosphate dehydrogenase isoenzymes. twenty-two electrophoretic types were identified, a result in agreement with the phenotyp ...199910555375
genetic variation among european strains of saccharomyces paradoxus: results from dna fingerprinting.we used microsatellite fingerprinting and rapd analysis to characterize 28 wild european strains of saccharomyces paradoxus. in contrast to our results from a previous allozyme survey [naumov et al. int. j. syst. bacteriol. 47: 341-344 (1997a)], these methods revealed extensive genetic variation. the rapd primers 5'aatcgggctg and 5'gggtaacgcc and the microsatellite primer (gtg)5 yielded reproducible amplification patterns of sufficient clarity and variability to distinguish individual strains fr ...200010879982
three new species in the saccharomyces sensu stricto complex: saccharomyces cariocanus, saccharomyces kudriavzevii and saccharomyces mikatae.on the basis of genetic analysis, molecular karyotyping and sequence analyses of the 18s rrna and internal transcribed spacer (its) region, three new saccharomyces species are described, saccharomyces cariocanus (with type strain ncyc 2890t), saccharomyces kudriavzevii (with type strain ncyc 2889t) and saccharomyces mikatae (with type strain ncyc 2888t). genetic and molecular analyses did not confirm the previously observed conspecificity of saccharomyces paradoxus and s. cariocanus. the latter ...200011034507
transcription of muts- and mutl-homologous genes during meiosis in saccharomyces cerevisiae and identification of a regulatory cis-element for meiotic induction of msh2.we have analysed the levels of mrna transcripts of the muts- and mutl-homologous genes of the yeast saccharomyces cerevisiae during the course of meiosis, by quantitative rt-pcr. we found that all muts homologues (msh1-6) were induced during meiosis, whereas no evidence for regulation of the mutl homologues (pms1, mlh1-3) was obtained. temporal expression patterns indicative of co-regulation were observed for the gene pairs msh4/msh5 and msh2/ spo11. sequence comparisons of the 5' flanking regio ...200111523800
ty5 gag mutations increase retrotransposition and suggest a role for hydrogen bonding in the function of the nucleocapsid zinc finger.the ty5 retrotransposon of saccharomyces paradoxus transposes in saccharomyces cerevisiae at frequencies 1,000-fold lower than do the native ty1 elements. the low transposition activity of ty5 could be due to differences in cellular environments between these yeast species or to naturally occurring mutations in ty5. by screening of a ty5 mutant library, two single mutants (d252n and y68c) were each found to increase transposition approximately sixfold. when combined, transposition increased 36-f ...200211884548
conservation of a portion of the s. cerevisiae ure2p prion domain that interacts with the full-length protein.the [ure3] prion of saccharomyces cerevisiae is a self-propagating inactive amyloid form of the ure2 protein. ure2p residues 1-65 constitute the prion domain, and the remaining c-terminal portion regulates nitrogen catabolism. we have examined the ure2 genes of wild-type isolates of s. cerevisiae and those of several pathogenic yeasts and a filamentous fungus. we find that the normal function of the s. cerevisiae ure2p in nitrogen regulation is fully complemented by the ure2p of candida albicans ...200212177423
identification and characterization of saccharomyces cerevisiae and saccharomyces paradoxus strains isolated from croatian vineyards.the identification, differentiation and characterization of indigenous saccharomyces sensu stricto strains isolated from croatian vineyards and the evaluation of their oenological potential.200212358693
hybrid speciation in experimental populations of yeast.most models of speciation require gradual change and geographic or ecological isolation for new species to arise. homoploid hybrid speciation occurred readily between saccharomyces cerevisiae and saccharomyces paradoxus. hybrids had high self-fertility (about 82%), low fertility when backcrossed to either parental species (about 7.5%), and vigorous growth under different thermal environments that favored one or the other of the parental species. extensive karyotypic changes (tetrasomy) were obse ...200212459586
engineering evolution to study speciation in yeasts.the saccharomyces 'sensu stricto' yeasts are a group of species that will mate with one another, but interspecific pairings produce sterile hybrids. a retrospective analysis of their genomes revealed that translocations between the chromosomes of these species do not correlate with the group's sequence-based phylogeny (that is, translocations do not drive the process of speciation). however, that analysis was unable to infer what contribution such rearrangements make to reproductive isolation be ...200312621434
differential malic acid degradation by selected strains of saccharomyces during alcoholic produce a high-quality wine, it is important to obtain a fine balance between the various chemical constituents, especially between the sugar and acid content. the latter is more difficult to achieve in wines that have high acidity due to excess malic acid, since wine yeast in general cannot effectively degrade malic acid during alcoholic fermentation. an indigenous saccharomyces paradoxus strain ro88 was able to degrade 38% of the malic acid in chardonnay must and produced a wine of good qua ...200312672592
saccharomyces cerevisiae and saccharomyces paradoxus coexist in a natural woodland site in north america and display different levels of reproductive isolation from european conspecifics.we report the isolation of multiple strains of saccharomyces cerevisiae and saccharomyces paradoxus from a natural woodland site in southeastern pennsylvania, usa, using enrichment culturing in a medium containing 7.6% (v/v) ethanol. the method was applied to bark and flux material collected from broad-leaved trees (mostly quercus spp.) and to associated soils. many candidate wild strains of saccharomyces were isolated using this method, most of them from soils associated with oaks. matings to g ...200212702333
distribution and sequence analysis of a novel ty3-like element in natural saccharomyces paradoxus isolates.little is known about the transposable elements of species closely related to saccharomyces cerevisiae. we present a novel transposable element in saccharomyces paradoxus, a close congener of s. cerevisiae. sequence analysis of this element, designated ty3-1p, indicates that it is a homologue of the s. cerevisiae ty3 element. ty3-1p shares 82% nucleotide identity with an s. cerevisiae ty3 element and appears to be structured identically to ty3, containing two overlapping open reading frames, six ...200312845602
conservation of the prion properties of ure2p through evolution.the yeast inheritable [ure3] element corresponds to a prion form of the nitrogen catabolism regulator ure2p. we have isolated several orthologous ure2 genes in different yeast species: saccharomyces paradoxus, s. uvarum, kluyveromyces lactis, candida albicans, and schizosaccharomyces pombe. we show here by in silico analysis that the gst-like functional domain and the prion domain of the ure2 proteins have diverged separately, the functional domain being more conserved through the evolution. the ...200312925776
isolation and characterization of the ho gene from the yeast saccharomyces paradoxus.a dna fragment homologous to the homothallism (ho) gene of saccharomyces cerevisiae was isolated from saccharomyces paradoxus and was found to contain an open reading frame that was 90.9% identical to the coding sequence of the s. cerevisiae ho gene. the putative ho gene was shown to induce diploidization in a heterothallic haploid strain from s. cerevisiae. phylogenetic analysis revealed that the coding and 5'-upstream regulatory regions from five saccharomyces sensu stricto ho genes have coevo ...200314554196
the efficiency of functional mitochondrial replacement in saccharomyces species has directional character.optimal interactions among nuclear and mitochondria-coded proteins are required to assemble functional complexes of mitochondrial oxidative phosphorylation. the communication between the nuclear and mitochondrial genomes has been studied by transplacement of mitochondria from related species into mutants devoid of mitochondrial dna (rho0). recently we have reported that the mitochondria transferred from saccharomyces paradoxus restored partially the respiration in saccharomyces cerevisiae rho0 m ...200314554201
eukaryotic regulatory element conservation analysis and identification using comparative genomics.comparative genomics is a promising approach to the challenging problem of eukaryotic regulatory element identification, because functional noncoding sequences may be conserved across species from evolutionary constraints. we systematically analyzed known human and saccharomyces cerevisiae regulatory elements and discovered that human regulatory elements are more conserved between human and mouse than are background sequences. although s. cerevisiae regulatory elements do not appear to be more c ...200414993210
population genetics of the wild yeast saccharomyces paradoxus.saccharomyces paradoxus is the closest known relative of the well-known s. cerevisiae and an attractive model organism for population genetic and genomic studies. here we characterize a set of 28 wild isolates from a 10-km(2) sampling area in southern england. all 28 isolates are homothallic (capable of mating-type switching) and wild type with respect to nutrient requirements. nine wild isolates and two lab strains of s. paradoxus were surveyed for sequence variation at six loci totaling 7 kb, ...200415020405
analysis of a ty1-less variant of saccharomyces paradoxus: the gain and loss of ty1 elements.because ty elements transpose through an rna intermediate, element accumulation through retrotransposition must be regulated or offset by element loss to avoid uncontrolled genome expansion. here we examine the fate of ty sequences in saccharomyces strain 337, a strain that is reported to lack ty1 and ty2 elements, but contains remnant solo long terminal repeats (ltrs). although strain 337 was initially classified as saccharomyces cerevisiae, our work indicates that this strain is more closely r ...200415197730
variation in the pattern of synonymous and nonsynonymous difference between two fungal genomes.the proportion of synonymous nucleotide differences per synonymous site (p(s)) and the proportion of nonsynonymous differences per nonsynonymous site (p(n)) were computed at 1,993,217 individual codons in 4,133 protein-coding genes between the two yeast species saccharomyces cerevisiae and saccharomyces paradoxus. when the modified nei-gojobori method was used, significantly more codons with p(n) > p(s) were observed than expected, based on random pairing of observed p(s) and p(n) values. howeve ...200515746015
[molecular polymorphism of viral dsrna of yeast saccharomyces paradoxus].an analysis of 53 strains of yeast saccharomyces paradoxus (ysp) of different geographic origins enabled us, for the first time, to find viral double-stranded rna (l and m fractions) in ysp and to study natural polymorphism. as in the cultured scerevisiae, the size of l dsrna was constant (4.5 kb). the size of minor m dsrna varied from 1.5 to 2.4 k.b. in ysp, we determined 7 types of m dsrna (m1-m7), which were not connected with the source of isolation or geographic origin of the host strains.200515790033
the [ure3] prion is not conserved among saccharomyces species.the [ure3] prion of saccharomyces cerevisiae is a self-propagating inactive form of the nitrogen catabolism regulator ure2p. to determine whether the [ure3] prion is conserved in s. cerevisiae-related yeast species, we have developed genetic tools allowing the detection of [ure3] in saccharomyces paradoxus and saccharomyces uvarum. we found that [ure3] is conserved in s. uvarum. in contrast, [ure3] was not detected in s. paradoxus. the inability of s. paradoxus ure2p to switch to a prion isoform ...200515956663
[first isolation of the yeast saccharomyces paradoxus in western siberia].two ascomycetous yeast strains have been isolated near novosibirsk from oak exudate. the strains have been identified as saccharomyces paradoxus bachinskaya based on the results of biochemical tests. the conspecificity of the isolates with s. paradoxus was confirmed by electrophoretic karyotyping and restriction analysis of the its region of its rdna. this first isolation of s. paradoxus in siberia provides evidence for the continuity of its natural habitats.200516211858
rapid identification and enumeration of saccharomyces cerevisiae cells in wine by real-time pcr.despite the beneficial role of saccharomyces cerevisiae in the food industry for food and beverage production, it is able to cause spoilage in wines. we have developed a real-time pcr method to directly detect and quantify this yeast species in wine samples to provide winemakers with a rapid and sensitive method to detect and prevent wine spoilage. specific primers were designed for s. cerevisiae using the sequence information obtained from a cloned random amplified polymorphic dna band that dif ...200516269715
population genomic analysis of outcrossing and recombination in yeast.the budding yeast saccharomyces cerevisiae has been used by humans for millennia to make wine, beer and bread. more recently, it became a key model organism for studies of eukaryotic biology and for genomic analysis. however, relatively little is known about the natural lifestyle and population genetics of yeast. one major question is whether genetically diverse yeast strains mate and recombine in the wild. we developed a method to infer the evolutionary history of a species from genome sequence ...200616892060
on the varied pattern of evolution of 2 fungal genomes: a critique of hughes and friedman.a number of statistical tests have been proposed to detect positive darwinian selection affecting a few amino acid sites in a protein, exemplified by an excess of nonsynonymous nucleotide substitutions. these tests are often more powerful than pairwise sequence comparison, which averages synonymous (d(s)) and nonsynonymous (d(n)) rates over the whole gene. in a recent study, however, hughes al and friedman r (2005. variation in the pattern of synonymous and nonsynonymous difference between two f ...200616982818
the spatial scale of genetic differentiation in a model organism: the wild yeast saccharomyces paradoxus.little information is presently available on the factors promoting genetic divergence in eukaryotic microbes. we studied the spatial distribution of genetic variation in saccharomyces paradoxus, the wild relative of saccharomyces cerevisiae, from the scale of a few centimetres on individual oak trees to thousands of kilometers across different continents. genealogical analysis of six loci shows that isolates from europe form a single recombining population, and within this population genetic dif ...200617028086
positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis.transposable elements have clearly played a major role in shaping both the size and organization of eukaryotic genomes. however, the evolution of essential genes in core biological processes may also have been shaped by coevolution with these elements. this would be predicted to occur in instances where host proteins are either hijacked for use by mobile elements or recruited to defend against them. to detect such cases, we have used the saccharomyces cerevisiae-saccharomyces paradoxus sibling s ...200617101967
mate choice assays and mating propensity differences in natural yeast sexual microbes, mating occurs by fusion of individual cells. this complete fitness investment suggests that cell behaviour could potentially mediate prezygotic isolation between microbial species, a topic about which very little is known. to investigate this possibility, we conducted individual cell mate choice trials and mass-culture mating propensity assays with isolates from sympatric natural populations of the closely related yeasts saccharomyces cerevisiae and saccharomyces paradoxus. a ...200617148286
prion species barrier between the closely related yeast proteins is detected despite coaggregation.prions are self-perpetuating and, in most cases, aggregation-prone protein isoforms that transmit neurodegenerative diseases in mammals and control heritable traits in yeast. prion conversion requires a very high level of identity of the interacting protein sequences. decreased transmission of the prion state between divergent proteins is termed "species barrier" and was thought to occur because of the inability of divergent prion proteins to coaggregate. species barrier can be overcome in cross ...200717296932
a screen for recessive speciation genes expressed in the gametes of f1 hybrid yeast.diploid hybrids of saccharomyces cerevisiae and its closest relative, saccharomyces paradoxus, are viable, but the sexual gametes they produce are not. one of several possible causes of this gamete inviability is incompatibility between genes from different species--such incompatible genes are usually called "speciation genes." in diploid f1 hybrids, which contain a complete haploid genome from each species, the presence of compatible alleles can mask the effects of (recessive) incompatible spec ...200717305429
allopatric divergence, secondary contact, and genetic isolation in wild yeast plants and animals, new biological species clearly have arisen as a byproduct of genetic divergence in allopatry. however, our understanding of the processes that generate new microbial species remains limited [1] despite the large contribution of microbes to the world's biodiversity. a recent hypothesis claims that microbes lack biogeographical divergence because their population sizes are large and their migration rates are presumably high [2, 3]. in recapitulating the classic microbial-eco ...200717306538
[massive isolation and identification of saccharomyces paradoxus yeasts from plant phyllosphere].year-round studies of epiphytic yeast communities revealed that the number of ascosporogenous yeasts of the genus saccharomyces inhabiting living and decaying leaves of some plants increased considerably in certain short periods (at the beginning of summer and in winter). massive isolation of saccharomycetes was performed from 11 plant species; earlier, these yeasts had been revealed mainly in sugar-rich substrates. the isolates were identified as saccharomyces paradoxus based on their physiolog ...200717583221
identification and characterization of amidase- homologous ami1 genes of bottom-fermenting has been proposed that a bottom-fermenting yeast strain of saccharomyces pastorianus is a natural hybrid between s. cerevisiae and s. bayanus and possesses at least two types of genome. in the process of conducting expressed sequence tag (est) analysis, we isolated bottom-fermenting yeast-specific (bfy) genes that have no significant homology with sequences in the s288c database. one of the bfy genes, ami1, encodes a protein with homology to an amidase conserved among plants, bacillus subtili ...200717924455
prezygotic reproductive isolation between saccharomyces cerevisiae and saccharomyces paradoxus.matings between different saccharomyces sensu stricto yeast species produce sexually sterile hybrids, so individuals should avoid mating with other species. any mechanism that reduces the frequency of interspecific matings will confer a selective advantage. here we test the ability of two closely-related saccharomyces sensu stricto species to select their own species as mates and avoid hybridisation.200818179683
population genomics of the wild yeast saccharomyces paradoxus: quantifying the life cycle.most microbes have complex life cycles with multiple modes of reproduction that differ in their effects on dna sequence variation. population genomic analyses can therefore be used to estimate the relative frequencies of these different modes in nature. the life cycle of the wild yeast saccharomyces paradoxus is complex, including clonal reproduction, outcrossing, and two different modes of inbreeding. to quantify these different aspects we analyzed dna sequence variation in the third chromosome ...200818344325
rapid evolution of yeast centromeres in the absence of find the most rapidly evolving regions in the yeast genome we compared most of chromosome iii from three closely related lineages of the wild yeast saccharomyces paradoxus. unexpectedly, the centromere appears to be the fastest-evolving part of the chromosome, evolving even faster than dna sequences unlikely to be under selective constraint (i.e., synonymous sites after correcting for codon usage bias and remnant transposable elements). centromeres on other chromosomes also show an elevated r ...200818430941
eukaryotic nuclear structure explains the evolutionary rate difference of ribosome export factors.because the nucleus is the cellular structure essentially differentiating eukaryotes from prokaryotes, the formation of the nuclear membrane should have been a key event in eukaryotic evolution. although an evolutionary cause of formation of the nucleus such as symbiosis has been speculated but still not clarified, evolutionary establishment of the transport system across the nuclear membrane must have been prerequisite for survival of the then-emerging eukaryotes. in particular, export of ribos ...200818588954
a multispecies-based taxonomic microarray reveals interspecies hybridization and introgression in saccharomyces cerevisiae.a multispecies-based taxonomic microarray targeting coding sequences of diverged orthologous genes in saccharomyces cerevisiae, saccharomyces paradoxus, saccharomyces mikatae, saccharomyces bayanus, saccharomyces kudriavzevii, naumovia castellii, lachancea kluyveri and candida glabrata was designed to allow identification of isolates of these species and their interspecies hybrids. analysis of isolates of several saccharomyces species and interspecies hybrids demonstrated the ability of the micr ...200919054123
population genomics of domestic and wild yeasts.since the completion of the genome sequence of saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. less well understood at the whole ...200919212322
the cellular concentration of the yeast ure2p prion protein affects its propagation as a prion.the [ure3] yeast prion is a self-propagating inactive form of the ure2p protein. we show here that ure2p from the species saccharomyces paradoxus (ure2p(sp)) can be efficiently converted into a prion form and propagate [ure3] when expressed in saccharomyces cerevisiae at physiological level. we found however that ure2p(sp) overexpression prevents efficient prion propagation. we have compared the aggregation rate and propagon numbers of ure2p(sp) and of s. cerevisiae ure2p (ure2p(sc)) in [ure3] c ...200919225154
complex adaptations can drive the evolution of the capacitor [psi], even with realistic rates of yeast sex.the [psi(+)] prion may enhance evolvability by revealing previously cryptic genetic variation, but it is unclear whether such evolvability properties could be favored by natural selection. sex inhibits the evolution of other putative evolvability mechanisms, such as mutator alleles. this paper explores whether sex also prevents natural selection from favoring modifier alleles that facilitate [psi(+)] formation. sex may permit the spread of "cheater" alleles that acquire the benefits of [psi(+)] ...200919521499
a comparative study of the wine fermentation performance of saccharomyces paradoxus under different nitrogen concentrations and glucose/fructose ratios.the main goal of the present study is to determine the effects of different nitrogen concentrations and glucose/fructose ratios on the fermentation performance of saccharomyces paradoxus, a nonconventional species used for winemaking.201019566722
generation of a large set of genetically tractable haploid and diploid saccharomyces strains.saccharomyces cerevisiae has proved to be an invaluable model in classical and molecular genetics studies. despite several hundreds of isolates already available, the scientific community relies on the use of only a handful of unrelated strains. the lack of sequence information, haploid derivatives and genetic markers has prevented novel strains from being used. here, we release a set of 55 s. cerevisiae and saccharomyces paradoxus genetically tractable strains, previously sequenced in the sacch ...200919840116
genetic identification of new biological species saccharomyces arboricolus wang et genetic testing for hybrid sterility unambiguously showed that the newly described yeast saccharomyces arboricolus wang et bai is reproductively isolated from saccharomyces cerevisiae, saccharomyces bayanus, saccharomyces cariocanus, saccharomyces kudriavzevii, saccharomyces mikatae and saccharomyces paradoxus and, therefore, represents a new biological species of the genus saccharomyces. combined phylogenetic analysis of the rdna repeat sequences (18s, 26s, its), nuclear act1 and mitocho ...201020379848
conservation of recombination hotspots in yeast.meiotic recombination does not occur randomly along a chromosome, but instead tends to be concentrated in small regions, known as "recombination hotspots." recombination hotspots are thought to be short-lived in evolutionary time due to their self-destructive nature, as gene conversion favors recombination-suppressing alleles over recombination-promoting alleles during double-strand repair. consistent with this expectation, hotspots in humans are highly dynamic, with little correspondence in loc ...201020385822
sporulation patterning and invasive growth in wild and domesticated yeast colonies.different cell types can form patterns within fungal communities; for example, colonies of saccharomyces cerevisiae form two sharply defined layers of sporulating cells separated by an intervening layer of unsporulated cells. because colony sporulation patterns have only been investigated in a single laboratory strain background (w303), in this report we examined these patterns in other strain backgrounds. two other laboratory strain backgrounds (sk1 and sigma1278b) that differ from w303 with re ...201020420901
widespread remodeling of mid-coding sequence nucleosomes by isw1.the positions of nucleosomes along eukaryotic dna are defined by the local dna sequence and are further tuned by the activity of chromatin remodelers. while the genome-wide effect of most remodelers has not been described, recent studies in saccharomyces cerevisiae have shown that isw2 prevents ectopic expression of anti-sense and suppressed transcripts at gene ends.201020459718
identifying gene clusters within localized regions in multiple important strategy to study genome evolution is to investigate the clustering of orthologous genes among multiple genomes, in which the most popular approaches require that the distance between adjacent genes in a cluster be small. we investigate a different formulation based on constraining the overall size of a cluster and develop statistical significance estimates that allow direct comparison of clusters of different sizes. we first consider a restricted version which requires that ortholo ...201020500020
saccharomyces paradoxus and saccharomyces cerevisiae reside on oak trees in new zealand: evidence for migration from europe and interspecies hybrids.saccharomyces cerevisiae and saccharomyces paradoxus are used as model systems for molecular, cell and evolutionary biology; yet we know comparatively little of their ecology. one niche from which these species have been isolated is oak bark. there are no reports of these species from oak in the southern hemisphere. we describe the recovery of both s. cerevisiae and s. paradoxus from oak in new zealand (nz), and provide evidence for introgression between the species. genetic inference shows that ...201020868381
discrimination of saccharomyces cerevisiae and saccharomyces paradoxus strains by the suc2 gene sequences. 201020953100
transcriptional network structure has little effect on the rate of regulatory evolution in yeast.studies in evolutionary developmental biology suggest that the structure of genetic pathways may bias the fixation of natural variation towards particular nodes in these pathways. in an attempt to test this trend genome-wide, we integrated several previously published datasets to examine whether the position of genes in the whole-genome transcriptional network of s. cerevisiae is associated with the amount of cis-regulatory expression divergence between s. cerevisiae and its sibling species s. p ...201020966117
relationship between prion propensity and the rates of individual molecular steps of fibril assembly.peptides and proteins possess an inherent propensity to self-assemble into generic fibrillar nanostructures known as amyloid fibrils, some of which are involved in medical conditions such as alzheimer disease. in certain cases, such structures can self-propagate in living systems as prions and transmit characteristic traits to the host organism. the mechanisms that allow certain amyloid species but not others to function as prions are not fully understood. much progress in understanding the prio ...201121233211
the fibrils of ure2p homologs from saccharomyces cerevisiae and saccharoymyces paradoxus have similar cross-ß structure in both dried and hydrated forms.the ability to convert into amyloid fibrils is a common feature of prion proteins. however, not all amyloid-forming proteins act as prions. here, we compared two homologs of the yeast prion protein ure2 from saccharomyces cerevisiae and saccharomyces paradoxus, scure2p and spure2p, which have different prion propensities in vivo. we also addressed the controversial issue of whether hydrated fibrils of ure2 show a fundamentally different x-ray diffraction pattern than dried samples. using fourier ...201121419850
genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in saccharomyces paradoxus.background. to characterize the genetic basis of phenotypic evolution, numerous studies have identified individual genes that have likely evolved under natural selection. however, phenotypic changes may represent the cumulative effect of similar evolutionary forces acting on functionally related groups of genes. phylogenetic analyses of divergent yeast species have identified functional groups of genes that have evolved at significantly different rates, suggestive of differential selection on th ...201121478372
comparative characterization of endo-polygalacturonase (pgu1) from saccharomyces cerevisiae and saccharomyces paradoxus under winemaking strains of saccharomyces cerevisiae have no to weak natural pectinase activity, despite their genetic ability to secrete an endo-polygalacturonase. the addition of external pectinase of fungal origin has therefore become a common step of winemaking in order to enhance the extraction of compounds located in the grape berry skins during maceration and to ease wine clarification after maturation. recently, the strong pectinase activity of a wine strain of saccharomyces paradoxus has been repor ...201121479715
the yeast irc7 gene encodes a β-lyase responsible for production of the varietal thiol 4-mercapto-4-methylpentan-2-one in wine.three varietal thiols are key aroma compounds in sauvignon blanc wines: 4-mercapto-4-methylpentan-2-one (4mmp), 3-mercaptohexanol (3mh) and its acetylated derivative 3-mercaptohexyl acetate (3mha). screening of saccharomyces cerevisiae strains identified a clinical isolate with elevated 4mmp production after fermentation. bulked segregant analysis of a cross between this isolate and the laboratory strain revealed a single major locus for 4mmp production near the telomere of chromosome 6. deletio ...201121569935
proteome-wide evidence for enhanced positive darwinian selection within intrinsically disordered regions in proteins.abstract: background: understanding the adaptive changes that alter the function of proteins during evolution is an important question for biology and medicine. the increasing number of completely sequenced genomes from closely related organisms, as well as individuals within species, facilitates systematic detection of recent selection events by means of comparative genomics. results: we have used genome-wide strain-specific single nucleotide polymorphism data from 64 strains of budding yeast ( ...201121771306
evidence for a high mutation rate at rapidly evolving yeast centromeres.abstract: background: although their role in cell division is essential, centromeres evolve rapidly in animals, plants and yeasts. unlike the complex centromeres of plants and aminals, the point centromeres of saccharomcyes yeasts can be readily sequenced to distinguish amongst the possible explanations for fast centromere evolution. results: using dna sequences of all 16 centromeres from 34 strains of saccharomyces cerevisiae and population genomic data from saccharomyces paradoxus, i show that ...201121767380
the rise of yeast population genomics.genome sequences of multiple individuals are essential to determine the forces shaping sequence variation as well as to understand the relationship between genotype and phenotype. because of their wide ecological, geographical and genetic diversity, yeast species represent an ideal model system for population genomics. recently, there has been a renewed interest in characterizing the genetic diversity within yeast species such as saccharomyces cerevisiae and saccharomyces paradoxus. here, we rev ...201121819942
Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences.The genome-sequencing gold rush has facilitated the use of comparative genomics to uncover patterns of genome evolution, although their causal mechanisms remain elusive. One such trend, ubiquitous to prokarya and eukarya, is the association of insertion/deletion mutations (indels) with increases in the nucleotide substitution rate extending over hundreds of base pairs. The prevailing hypothesis is that indels are themselves mutagenic agents. Here, we employ population genomics data from Escheric ...201121697975
divergence in wine characteristics produced by wild and domesticated strains of saccharomyces cerevisiae.the budding yeast saccharomyces cerevisiae is the primary species used by wine makers to convert sugar into alcohol during wine fermentation. saccharomyces cerevisiae is found in vineyards, but is also found in association with oak trees and other natural sources. although wild strains of s. cerevisiae as well as other saccharomyces species are also capable of wine fermentation, a genetically distinct group of s. cerevisiae strains is primarily used to produce wine, consistent with the idea that ...201122093681
genomic structure of and genome-wide recombination in the saccharomyces cerevisiae s288c progenitor isolate em93.the diploid isolate em93 is the main ancestor to the widely used saccharomyces cerevisiae haploid laboratory strain, s288c. in this study, we generate a high-resolution overview of the genetic differences between em93 and s288c. we show that em93 is heterozygous for >45,000 polymorphisms, including large sequence polymorphisms, such as deletions and a saccharomyces paradoxus introgression. we also find that many large sequence polymorphisms (lsps) are associated with ty-elements and sub-telomeri ...201121966457
a multiplex set of species-specific primers for rapid identification of members of the genus saccharomyces.the saccharomyces genus (previously saccharomyces sensu stricto) formally comprises saccharomyces arboricola, saccharomyces bayanus, saccharomyces cariocanus, saccharomyces cerevisiae, saccharomyces kudriavzevii, saccharomyces mikatae, saccharomyces paradoxus and saccharomyces pastorianus. species-specific primer pairs that produce a single band of known and different product size have been developed for each member of the clade with the exception of s. pastorianus, which is a polyphyletic allop ...201122093682
nature and distribution of large sequence polymorphisms in saccharomyces obtain a better understanding of the genome-wide distribution and the nature of large sequence polymorphisms (lsps) in saccharomyces cerevisiae, we hybridized genomic dna of 88 haploid or homozygous diploid s. cerevisiae strains of diverse geographic origins and source substrates onto high-density tiling arrays. on the basis of loss of hybridization, we identified 384 lsps larger than 500 bp that were located in 188 non-overlapping regions of the genome. validation by polymerase chain reactio ...201122093685
prezygotic isolation between saccharomyces cerevisiae and saccharomyces paradoxus through differences in mating speed and germination timing.although prezygotic isolation between sympatric populations of closely related animal and plant species is well documented, far less is known about such evolutionary phenomena in sexual microbial species, as most are difficult to culture and manipulate. using the molecular and genetic tools available for the unicellular fungus saccharomyces cerevisiae, and applying them to s. paradoxus, we tested the behavior of individual cells from sympatric woodland populations of both species for evidence of ...201122486698
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