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Genomic Structure of and Genome-Wide Recombination in the Saccharomyces cerevisiae S288C Progenitor Isolate EM93  [PDF]
Anders Esberg, Ludo A. H. Muller, John H. McCusker
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0025211
Abstract: 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-telomeric regions. We identified 2,965 genetic markers, which we then used to genotype 120 EM93 tetrads. In addition to deducing the structures of all EM93 chromosomes, we estimate that the average EM93 meiosis produces 144 detectable recombination events, consisting of 87 crossover and 31 non-crossover gene conversion events. Of the 50 polymorphisms showing the highest levels of non-crossover gene conversions, only three deviated from parity, all of which were near heterozygous LSPs. We find that non-telomeric heterozygous LSPs significantly reduce meiotic recombination in adjacent intervals, while sub-telomeric LSPs have no discernable effect on recombination. We identified 203 recombination hotspots, relatively few of which are hot for both non-crossover gene conversions and crossovers. Strikingly, we find that recombination hotspots show limited conservation. Some novel hotspots are found adjacent to heterozygous LSPs that eliminate other hotspots, suggesting that hotspots may appear and disappear relatively rapidly.
Bulk Segregant Analysis by High-Throughput Sequencing Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae  [PDF]
Jared W. Wenger,Katja Schwartz,Gavin Sherlock
PLOS Genetics , 2010, DOI: 10.1371/journal.pgen.1000942
Abstract: Fermentation of xylose is a fundamental requirement for the efficient production of ethanol from lignocellulosic biomass sources. Although they aggressively ferment hexoses, it has long been thought that native Saccharomyces cerevisiae strains cannot grow fermentatively or non-fermentatively on xylose. Population surveys have uncovered a few naturally occurring strains that are weakly xylose-positive, and some S. cerevisiae have been genetically engineered to ferment xylose, but no strain, either natural or engineered, has yet been reported to ferment xylose as efficiently as glucose. Here, we used a medium-throughput screen to identify Saccharomyces strains that can increase in optical density when xylose is presented as the sole carbon source. We identified 38 strains that have this xylose utilization phenotype, including strains of S. cerevisiae, other sensu stricto members, and hybrids between them. All the S. cerevisiae xylose-utilizing strains we identified are wine yeasts, and for those that could produce meiotic progeny, the xylose phenotype segregates as a single gene trait. We mapped this gene by Bulk Segregant Analysis (BSA) using tiling microarrays and high-throughput sequencing. The gene is a putative xylitol dehydrogenase, which we name XDH1, and is located in the subtelomeric region of the right end of chromosome XV in a region not present in the S288c reference genome. We further characterized the xylose phenotype by performing gene expression microarrays and by genetically dissecting the endogenous Saccharomyces xylose pathway. We have demonstrated that natural S. cerevisiae yeasts are capable of utilizing xylose as the sole carbon source, characterized the genetic basis for this trait as well as the endogenous xylose utilization pathway, and demonstrated the feasibility of BSA using high-throughput sequencing.
Genome sequencing and genetic breeding of a bioethanol Saccharomyces cerevisiae strain YJS329  [cached]
Zheng Dao-Qiong,Wang Pin-Mei,Chen Jie,Zhang Ke
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-479
Abstract: Background Environmental stresses and inhibitors encountered by Saccharomyces cerevisiae strains are the main limiting factors in bioethanol fermentation. Strains with different genetic backgrounds usually show diverse stress tolerance responses. An understanding of the mechanisms underlying these phenotypic diversities within S. cerevisiae populations could guide the construction of strains with desired traits. Results We explored the genetic characteristics of the bioethanol S. cerevisiae strain YJS329 and elucidated how genetic variations in its genome were correlated with specified traits compared to similar traits in the S288c-derived strain, BYZ1. Karyotypic electrophoresis combined with array-comparative genomic hybridization indicated that YJS329 was a diploid strain with a relatively constant genome as a result of the fewer Ty elements and lack of structural polymorphisms between homologous chromosomes that it contained. By comparing the sequence with the S288c genome, a total of 64,998 SNPs, 7,093 indels and 11 unique genes were identified in the genome of YJS329-derived haploid strain YJSH1 through whole-genome sequencing. Transcription comparison using RNA-Seq identified which of the differentially expressed genes were the main contributors to the phenotypic differences between YJS329 and BYZ1. By combining the results obtained from the genome sequences and the transcriptions, we predicted how the SNPs, indels and chromosomal copy number variations may affect the mRNA expression profiles and phenotypes of the yeast strains. Furthermore, some genetic breeding strategies to improve the adaptabilities of YJS329 were designed and experimentally verified. Conclusions Through comparative functional genomic analysis, we have provided some insights into the mechanisms underlying the specific traits of the bioenthanol strain YJS329. The work reported here has not only enriched the available genetic resources of yeast but has also indicated how functional genomic studies can be used to improve genetic breeding in yeast.
Construction of killer industrial yeast Saccharomyces cerevisiae HAU-1 and its fermentation performance
Bajaj, Bijender K.;Sharma, S.;
Brazilian Journal of Microbiology , 2010, DOI: 10.1590/S1517-83822010000200030
Abstract: saccharomyces cerevisiae hau-1, a time tested industrial yeast possesses most of the desirable fermentation characteristics like fast growth and fermentation rate, osmotolerance, high ethanol tolerance, ability to ferment molasses, and to ferment at elevated temperatures etc. however, this yeast was found to be sensitive against the killer strains of saccharomyces cerevisiae. in the present study, killer trait was introduced into saccharomyces cerevisiae hau-1 by protoplast fusion with saccharomyces cerevisiae mtcc 475, a killer strain. the resultant fusants were characterized for desirable fermentation characteristics. all the technologically important characteristics of distillery yeast saccharomyces cerevisiae hau-1 were retained in the fusants, and in addition the killer trait was also introduced into them. further, the killer activity was found to be stably maintained during hostile conditions of ethanol fermentations in dextrose or molasses, and even during biomass recycling.
Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains  [PDF]
Joseph Schacherer, Douglas M. Ruderfer, David Gresham, Kara Dolinski, David Botstein, Leonid Kruglyak
PLOS ONE , 2007, DOI: 10.1371/journal.pone.0000322
Abstract: Ten years have passed since the genome of Saccharomyces cerevisiae–more precisely, the S288c strain–was completely sequenced. However, experimental work in yeast is commonly performed using strains that are of unknown genetic relationship to S288c. Here, we characterized the nucleotide-level similarity between S288c and seven commonly used lab strains (A364A, W303, FL100, CEN.PK, ∑1278b, SK1 and BY4716) using 25mer oligonucleotide microarrays that provide complete and redundant coverage of the ~12 Mb Saccharomyces cerevisiae genome. Using these data, we assessed the frequency and distribution of nucleotide variation in comparison to the sequenced reference genome. These data allow us to infer the relationships between experimentally important strains of yeast and provide insight for experimental designs that are sensitive to sequence variation. We propose a rational approach for near complete sequencing of strains related to the reference using these data and directed re-sequencing. These data and new visualization tools are accessible online in a new resource: the Yeast SNPs Browser (YSB; http://gbrowse.princeton.edu/cgi-bin/gbr?owse/yeast_strains_snps) that is available to all researchers.
Evolutionary Genomics of Transposable Elements in Saccharomyces cerevisiae  [PDF]
Martin Carr, Douda Bensasson, Casey M. Bergman
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0050978
Abstract: Saccharomyces cerevisiae is one of the premier model systems for studying the genomics and evolution of transposable elements. The availability of the S. cerevisiae genome led to unprecedented insights into its five known transposable element families (the LTR retrotransposons Ty1-Ty5) in the years shortly after its completion. However, subsequent advances in bioinformatics tools for analysing transposable elements and the recent availability of genome sequences for multiple strains and species of yeast motivates new investigations into Ty evolution in S. cerevisiae. Here we provide a comprehensive phylogenetic and population genetic analysis of all Ty families in S. cerevisiae based on a systematic re-annotation of Ty elements in the S288c reference genome. We show that previous annotation efforts have underestimated the total copy number of Ty elements for all known families. In addition, we identify a new family of Ty3-like elements related to the S. paradoxus Ty3p which is composed entirely of degenerate solo LTRs. Phylogenetic analyses of LTR sequences identified three families with short-branch, recently active clades nested among long branch, inactive insertions (Ty1, Ty3, Ty4), one family with essentially all recently active elements (Ty2) and two families with only inactive elements (Ty3p and Ty5). Population genomic data from 38 additional strains of S. cerevisiae show that the majority of Ty insertions in the S288c reference genome are fixed in the species, with insertions in active clades being predominantly polymorphic and insertions in inactive clades being predominantly fixed. Finally, we use comparative genomic data to provide evidence that the Ty2 and Ty3p families have arisen in the S. cerevisiae genome by horizontal transfer. Our results demonstrate that the genome of a single individual contains important information about the state of TE population dynamics within a species and suggest that horizontal transfer may play an important role in shaping the genomic diversity of transposable elements in unicellular eukaryotes.
Using Magnetic Nanoparticles to Eliminate Oscillations in Saccharomyces cerevisiae Fermentation Processes  [PDF]
Lakshmi N. Sridhar
Journal of Sustainable Bioenergy Systems (JSBS) , 2012, DOI: 10.4236/jsbs.2012.23004
Abstract: This article provides computational evidence to show that functionalized magnetic nanoparticles can eliminate the wasteful oscillatory behavior in fermentation processes involving Saccharomyces cerevisiae. There has been a consi-derable amount of work demonstrating the existence of oscillations in fermentation processes. Recently Reference [1] computationally demonstrated very simple strategies to eliminate the oscillations in the fermentation process. In the case of the of the Saccharomyces cerevisiae fermentation process it was shown that the addition of a little bit of oxygen would be successful in eliminating the oscillation causing Hopf bifurcations. The work of [2,3] demonstrated that oxygen mass transfer could be enhanced by using functionalized magnetic nanoparticles. The aim of this work is to incorporate the model used by [3] regarding the enhancement of oxygen mass transfer in the cybernetic Jones Kompala model [4] describing the dynamics of the Saccharomnyces cerevisiae fermentation process and demonstrate that using the functionalized magnetic nanoparticles can by altering the mass transfer coefficient actually succeed in eliminating the oscillatory behavior that plagues the Saccharomyces cerevisiae fermentation process. This occurs because the oscillation causing Hopf bifurcations are sensitive to the amount of input oxygen and increasing the oxygen mass transfer coefficient causes the disappearance of the Hopf bifurcation points.
Functional States Recognition System for Fed-batch Cultivation of Saccharomyces cerevisiae  [PDF]
Ljakova K.,Pencheva T.
Bioautomation , 2008,
Abstract: Free software for entering and documenting data EpiData is here used for design of a system for functional states recognition during a fermentation process. The identification of the current process state is based on the predetermined rules, rendering specific metabolic mechanisms. Developed system is further applied for a fed-batch cultivation of Saccharomyces cerevisiae.
Interaction between Saccharomyces cerevisiae and chrysotile  [cached]
Cassiola F.,Silveira M.,Jericó S.,Joekes I.
European Cells and Materials (ECM) , 2001,
Abstract: The interaction between Saccharomyces cerevisiae and chrysotile fibers was studied by scanning electron microscopy. The yeast cells adhere preferentially to the fibrils. In the extreme case, all the adhered fibrils were broken, resulting in a complete coverage of the surface. The chrysotile covered cells showed less buds, but retained metabolic capacities, and were fully active in fermentation experiments after one year. The interaction degree was depending on contact time and adhesion medium. The longer the contact period, the stronger the interaction between the cells and the fibers. Cells adhered in water show poor entrapment after short contact time, but were highly entrapped after longer periods and did not show any agglomerates. Cells adhered in the presence of nutrients showed a lower entrapment and a higher degree of cellular growth.
Protein Enrichment of Cassava Pulp Fermentation by Saccharomyces cerevisiae
W. Kaewwongsa,S. Traiyakun,C. Yuangklang,C. Wachirapakorn,P. Paengkoum
Journal of Animal and Veterinary Advances , 2012, DOI: 10.3923/javaa.2011.2434.2440
Abstract: The purpose of this study was to determine intestinal digestibility of residual components of cassava pulp solid state fermentation by Saccharomyces cerevisiae for animal feed. Three ruminally cannulated animal were used to measure in situ rumen Dry Matter (DM) and Crude Protein (CP) degradability characteristics of cassava pulp solid state fermentation by S. cerevisiae. Nylon bags containing 3 g (as fed basis) of each feed was immersed in duplicate at each time point in the ventral rumen of each goat for 2, 4, 8, 12, 24, 48 and 72 h. Rumen feed residues from bags of 16 h incubation were used for estimation of lower gut digestibility by the technique of in vitro pepsin-pancreatin digestion. The results of the chemical analysis indicated that fermentation was slightly improved Ruminal Undegradable Protein (RUP) of cassava pulp. The highest value of RUP was significantly differ (p<0.05) after 5 days of fermentation period. Ruminal undegradable protein content increased (p<0.05) with the addition of S. cerevisiae in cassava pulp. The present results indicate that fermented cassava pulp can improve protein content and ruminal undegradable protein content.
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