Academic literature on the topic 'Saccharomyces sensu stricto complex'

Made available in DSpace on 2014-06-12T18:07:38Z (GMT). No. of bitstreams: 2 arquivo781_1.pdf: 980520 bytes, checksum: 129d41a77288e6f76ea015b1be222c70 (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2010
Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco
O complexo Saccharomyces sensu stricto é atualmente constituído por espécies de leveduras que correspondem aos epítetos Saccharomyces cerevisiae, Saccharomyces paradoxus, Saccharomyces bayanus, Saccharomyces cariocanus, Saccharomyces mikatae, Saccharomyces kudriavzevii, Saccharomyces pastorianus, Saccharomyces uvarum, Saccharomyces monacensis e Saccharomyces carlsbergensis. A grande similaridade fisiológica entre estas espécies decorre da alta semelhança genética que permite até a formação de híbridos interespecíficos que são viáveis, embora estéreis. Atualmente, os taxonomistas têm se utilizado das técnicas de biologia molecular para a identificação e diferenciação dos isolados deste grupo. Tais técnicas podem gerar valiosas informações sobre a composição e o arranjo genômico desse grupo de leveduras, permitindo o entendimento sobre os mecanismos de especiação biológica e de adaptação genética aos ambientes industriais. O objetivo deste trabalho foi tipar as leveduras deste complexo com o iniciador (GTG)5 para verificar o perfil molecular e realizar uma análise cariotípica de seus cromossomos através da eletroforese em campo pulsado (PFGE) e encontramos diferenças principalmente nas linhagens de S. bayanus tanto intra quanto interespecíficas em ambas as técnicas utilizadas e graças a estas técnicas foi percebido que a linhagem CLIB 811 foi classificada equivocadamente como S. bayanus tendo perfil fingerprinting e cariótipo de S. cerevisiae. Também foi verificado a composição alélica para os loci gênicos MET2, URA1, LEU2, HO, YCK1, RPS24A e SNF1 de S. bayanus e constatado que essa levedura possui genes que vieram de S. uvarum

Made available in DSpace on 2014-06-12T15:53:07Z (GMT). No. of bitstreams: 2 arquivo5192_1.pdf: 788582 bytes, checksum: 9c493ee2ba6857656c0a20883bb05c1f (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2006
A relação biológica de leveduras industrialmente importantes do complexo Saccharomyces sensu stricto causa equívoco na correta identificação das leveduras. Por isso, este trabalho apresenta a técnica de PCR - fingerprinting com diferentes marcadores que identificaram com eficiência as verdadeiras espécies do complexo Saccharomyces sensu stricto e indicaram os híbridos naturais isolados de processos industriais. Linhagens tipo, linhagens comerciais de vinho e leveduras isoladas de vinho artesanal foram submetidas à análise de PCR - fingerprinting usando oligonucleotídeos únicos (SPAR) e análise de restrição de genes ribossomais e estruturais. Todas as seis espécies reconhecidas do complexo Saccharomyces sensu stricto foram discriminadas e erros na taxonomia anterior das leveduras de vinho foram observados. Além disso, estes marcadores SPAR mostraram a complexidade da constituição híbrida dos isolados industriais. O uso de marcadores SPAR pode ajudar na identificação de leveduras isoladas da indústria e do meio ambiente dentre uma das seis espécies do complexo Saccharomyces sensu stricto e seus híbridos interespecíficos, e na reclassificação de linhagens depositadas em coleções de leveduras. Embora este conjunto de marcadores falhe em determinar a contribuição de parentais no processo de hibridização, pode eficientemente traçar a dispersão de leveduras híbridas que foram originadas em eventos simples de hibridização. O padrão único gerado pelos marcadores SPAR foi bastante eficiente no monitoramento da população de leveduras durante o processo de fermentação industrial e pode detectar a aproximação de leveduras híbridas em cada meio ambiente

El género Saccharomyces incluye tanto especies naturales como especies de levaduras que se utilizan en fermentaciones industriales y tradicionales. Algunas bebidas fermentadas, como son el Pulque y la Chicha, se obtienen mediante un proceso tradicional desarrollado durante el Neolítico americano en las civilizaciones precolombinas mesoamericanas y andinas. Por ello, las levaduras que participan en estos procesos de fermentación han estado aisladas de las poblaciones vínicas del resto del mundo, hasta la llegada de los europeos en 1942, con la introducción de nuevos procesos fermentativos, como son la producción de vino y los destilados. El objetivo del presente estudio fue determinar la variación genética de las cepas del género Saccharomyces, tanto presentes en fermentaciones tradicionales como las de procesos fermentativos industriales, para deducir el origen y la historia evolutiva de Saccharomyces cerevisiae. Con técnicas moleculares se detectó a S. cerevisiae y S. paradoxus en bebidas tradicionales de Latinoamérica, y mediante estudios fisiológicos se demostró que S. cerevisiae presenta propiedades tecnológicas adecuadas para una fermentación vínica. Con el análisis filogenético de cuatro regiones nucleares y una mitocondrial se detectó que S. cerevisiae esta compuesta por dos poblaciones, una de ambientes vínicos y la otra de ambientes no vínicos, muy diferentes entre ellas. Las poblaciones vínicas se caracterizan por ser un grupo muy homogéneo, con baja tasa de recombinación, alta frecuencia de homocigosis, con menos diversidad genotípica y menos divergencia nucleotídica. Esto indica una reciente domesticación, con reproducción clonal y sucesos de autodiploidización. En cambio, las poblaciones no vínicas están formadas por un grupo muy heterogéneo, con reproducción clonal pero la reproducción sexual más frecuente por anfimixis. La detección de alelos vínicos y no vínicos entre las cepas de las poblaciones latinoamericanas indica que existe flujo genético entre ambas poblaciones. Por otro lado, se detectó que los alelos vínicos de S. cerevisiae no provienen de S. paradoxus sino de los alelos no vínicos de S. cerevisiae. En base a los resultados obtenidos se proponen dos posibles escenarios no incompatibles para el origen de S. cerevisiae. En un primer escenario, las cepas no vínicas forman una población muy heterogénea con alelos muy diversos, lo que dio lugar a la aparición de las cepas vínicas por domesticación, y se vio reducida la diversidad genética cuando se fijaron los alelos vínicos. En el segundo caso, las cepas vínicas y no vínicas, son poblaciones con alelos muy diferentes, pero con flujo genético se intercambiaron alelos vínicos en no vínicos, pero muy raro en el otro sentido. Finalmente se proponen que al menos tres eventos de hibridación dieron origen a las cepas híbridas aisladas de vinos, y probablemente a partir de uno solo para las cepas híbridas cerveceras. Sin embargo, los fenómenos de recombinación y de introgresión detectados entre diferentes especies de Saccharomyces permiten suponer que la hibridación puede ocurrir con mayor frecuencia.
Traditional fermented beverages and foods from Latin America are poorly studied. The yeast microbiota involved in these ancient processes has been isolated from "Old World" yeast populations until the introduction of winemaking and distillation. The aim of this work was to study the genetic variation of Saccharomyces strains from traditional and industrial fermentations and to deduce the origin and evolution of S. cerevisiae. S. cerevisiae and S. paradoxus were isolated from traditional Latin American fermentations. Some of the investigated S. cerevisiae strains showed good physiological properties that are important in the wine production. A genetic analysis was performed based on sequencing of four nuclear and one mitochondrial gene of strains isolated from Latin-American traditional and industrial (mainly European) fermentative processes. Genetic variability from S. cerevisiae strains shows two populations, one from wine and the second from non-wine fermentations. Wine population represent a very homogeneous group, with low recombination rate, high frequency of homozygous strains, low genotypic diversity and low nucleotide divergence. These finding indicate a recent domestication event by clonal reproduction and some events of haplo-selfing. Non-wine populations represent a heterogeneous group, with clonal reproduction and rare sexual reproduction by anfimixis. Wine and non-wine alleles detected in Latin-American populations indicated genetic flow. Phylogenetic analysis shows that wine alleles of S. cerevisiae are originated from non-wine alleles of S. cerevisiae, but not from S. paradoxus. Two theories are proposed for the origin of wine S. cerevisiae strains: 1) wine yeast represent a population with low genetic diversity because "wine" alleles were fixed and emerged after domestication event from an ancestral and heterogeneous population of non-wine yeast; 2) wine and non-wine strains represent populations with different alleles, but genetic flow is frequent from wine to non-wine, and rare in opposite direction. Recombination and introgresion events detected in Saccharomyces species indicated that hybridizations occur more frequently then expected. According to the phylogenetic results wine hybrids S. cerevisiae x S. kudriavzevii were originated from three hybridizations events, and brewery hybrids from one.

Proposed dissertation thesis deals with wine and artisanal cheeses microbiology. The first part is focused on identification of yeasts isolated from grapes and musts during production of white and red wines. The grape varieties were grown under the integrated and organic farming on Moravian vineyard. Yeasts were identified by ITS-PCR-RFLP method (amplifying internal transcribed spacer ITS: ITS1, ITS2 and 5.8S rDNA) and unknown species were subjected to partial sequencing of ITS rDNA region. In total, 524 isolates were divided into 14 different species belonging to six genus were identified from. The first stages of fermentation process were characterised by predominance of non-saccharomyces species especially H. uvarum. Due to increased ethanol concentration strains of S. cerevisiae prevailed in the later phases of the process. Further, partial aim of this study was to isolate and to apply selected autochthonous S. cerevisiae strains as starter culture during controlled industrial wine fermentation process. Genus Saccharomyces was distinguished from other non-saccharomyces species by ITS-PCR-RFLP. Further, in order to distinguish Saccharomyces genus at the species and the strain level, several molecular methods were applied including PCR-fingerprinting (rep- and RAPD-PCR), species-specific primers (multiplex and touchdown PCR), LSU-DGGE and interdelta PCR. Species-specific primers enabled us to distinguish some species of the Saccharomyces sensu stricto complex. Furthermore, interdelta PCR seems to be useful tool for S. cerevisiae strains identification. Among 120 isolated autochthonous strains belonging to Saccharomyces genus, 45 different strains were identified. Based on its sufficient technological properties (osmo- and ethanol tolerance, low H2S production etc.), S. cerevisiae 1-09 strain isolated from grape berries coming from moravian vineyard was chosen. Strain S. cerevisiae 1-09 was tested in small amount of must and after that also during industrial fermentation of red and white wine production. Based on the results of chemical and sensorial analysis, the strain seems to be suitable for application as the starter culture for winemaking process. The final part of this thesis is focused on quantification and identification of the yeasts isolated from artisanal cheeses and their by-products coming from Western Balkan Countries. Isolated species were identified by ITS-PCR-RFLP, partial sequencing and by physiological tests. Among the 20 yeast species found, D. hansenii, C. zeylanoides and Y. lipolytica were found to be predominant. Moreover, we developed culture-independent, semi-quantitative technique based on construction of ITS-clone library from metagenomic DNA to investigate complex fungal communities associated with artisanal cheeses and their by-products. Novel technique is based on direct extraction of total DNA from the sample. This was compared with culture-dependent ITS-PCR-RFLP and culture-independent LSU-DGGE methods. The results highlighted the discrepancies among these methods. Finally, the divergences among applied methods were confirmed by correlation analysis and by indices of general biodiversity and dominance of species. ITS-clone library approach combines the advantages of cultivation-based analysis and LSU-DGGE with semi-quantification of fungal species without the requirement of their cultivation. This study might open new perspectives in direct and complex analysis of yeasts and moulds in food matrices.

Baker's yeast, Saccharomyces cerevisiae, is a well-studied model system in genetics and molecular biology. It is also a promising system for experimental ecology, evolution, and epidemiology, and is very important in the fermentation industry. The large amount of information generated by studies using this organism cannot be fully exploited until sufficient ecological data is gathered. Only when the natural environment of S. cerevisiae is well characterized can research using this yeast as a model system be put into context. The lack of information about the natural environment of S. cerevisiae is what prompted this work. First, I review the current available data on the ecology and evolution of S. cerevisiae and its sister species (the sensu stricto species complex). I then report results from fieldwork in an old growth forest. Finally, I report a community ecology experiment carried out using three naturally coexisting yeasts from this forest.

Transposable elements (TEs) are almost ubiquitous components of eukaryotic genomes that have long been considered solely deleterious or ’junk DNA’. They are split into two main forms, retro-transposons and DNA transposons, depending on the method of replication employed. Hosts have developed strategies for combating TEs including RNAi, methylation and copy number con-trol. TEs have also evolved ways of persisting in the genome in order to survive, such as target site specificity. Two additional ways which may be utilised by TEs, positive selection and horizontal transfer, were investigated here primarily using the budding yeasts in the Saccharomyces sensu lato complex. These species typically contain up to five families of retrotransposons, designatedTy1-5, and multiple subfamilies, all of varying transpositional activity. Discoveries of insertions evolving under positive selection and providing benefits to their hosts have been sporadic and serendipitous findings in a number of organisms. Full genome screenings for such insertions are rarely published, despite the impact TE insertions have upon their hosts. A population genomics approach was performed to address this issue in the genomes of Saccha-romyces cerevisiae and sister species S. paradoxus. Signatures of positive selection acting upon Ty insertions were identified using Tajima’s statistical D test. Neighbouring genes were also analysed to ascertain the true target of selection where hitchhiking linked the two. A subset of LTR-gene pairings were explored using qPCR in order to identify any effects on host gene expression the occupied loci may cause. Two genes displayed significantly increased levels of expression, which may be due to the presence of positive selection candidate LTRs, which in turn may contribute to improving host fitness. This thesis further documents the systematic screening for Ty-like elements of all available genomes of budding yeast and related species. Extensive phylogenetic analyses estimated evolutionary relationships and possible horizontal transfer events of elements between the species. Evidence for in excess of 75 horizontal transfer events was uncovered here, around half of which were successful in propagating in new genomes. The occurrence of horizontal transfer of TEs in the genomes of budding yeast is therefore far more common than previously documented. During screening of genomes, a further potential method of avoiding host defences was uncovered. The divergence of the highly active Ty4 family, which coincided with population isolation of multiple Saccharomyces species into subfamilies, was surprising given previous reports of this family being of particularly low activity. Such events are rarely recorded in eukaryotic genomes, and may also illustrate the compulsive spread of a new subfamily via horizontal transfer. The investigations reported here represent the first genomic screening of Ty insertions in Saccharomyces for signatures of positive selection, and an updated, comprehensive search for evidence of HT between species of budding yeast. Both may act as methods for TE families to persist in the genomes of their hosts, and represent far more than simply ’junk DNA’.