Ontology highlight
ABSTRACT:
PROVIDER: PRJNA612934 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11318247_1.fastq.gz | Fastqsanger.gz | |||
| SRR11318247_2.fastq.gz | Fastqsanger.gz | |||
| SRR11318248_1.fastq.gz | Fastqsanger.gz | |||
| SRR11318248_2.fastq.gz | Fastqsanger.gz | |||
| SRR11318249_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Laboratory evolution of Saccharomyces cerevisiae for improved methanol assimilation
| PRJNA612896 | ENA
Project description:Reprogramming a non-methylotrophic industrial host, such as Saccharomyces cerevisiae, to a synthetic methylotroph reprents a huge challenge due to the complex regulation in yeast. Through TMC strategy together with ALE strategy, we completed a strict synthetic methylotrophic yeast that could use methanol as the sole carbon source. However, how cells respond to methanol and remodel cellular metabolic network on methanol were not clear. Therefore, genome-scale transcriptional analysis was performed to unravel the cellular reprograming mechanisms underlying the improved growth phenotype.
2024-05-02 | GSE173802 | GEO
Project description:We study the genetics, including microarray karyotyping using comparative genomic hybridization, to explore global changes in the genomic DNA of seven S. cerevisiae strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNVs) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media.
2013-12-15 | GSE46165 | GEO
Project description:The environmental stresses and inhibitors encounted by Saccharomyces cerevisiae strains are main limiting factors in bioethanol fermentation. Investigation of the molecular mechanisms underlying the stresses-related phenotypes diversities within and between S. cerevisiae populations could guide the construction of yeast strains with improved stresses tolerance and fermentation performances. Here, we explored the genetic characteristics of the bioethanol S. cerevisiae strains, and elucidated the genetic variations correlated with its advantaged traits (higher ethanol yield under sever conditions and better tolerance to multiple stresses compared to an S288c derived laboratory strain BYZ1). Firstly, pulse-field gel electrophoresis combined with array-comparative genomic hybridization was used to compare the genome structure of industrial strains and the laboratory strain BYZ1.
2011-09-15 | GSE31872 | GEO
Project description:We study the genetics, including microarray karyotyping using comparative genomic hybridization to explore global changes in the genomic DNA, of four S. bayanus var uvarum strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNV) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media.
2016-04-15 | GSE67917 | GEO
Project description:We investigated the genome-wide distribution of Okazaki fragments in the commonly used laboratory Saccharomyces cerevisiae strain S288C to study the DNA replication model adopted by the budding yeast. The method based upon lambda exonuclease digestion for purification of RNA-primed replication intermediates was first improved to be suitable for the purification of Okazaki fragments. Then, we used this improved method to purify Okazaki fragments from S288C yeast cells, followed by Illumina sequencing. We found that the expected asymmetric distribution of Okazaki fragments around confirmed replication origins, which was derived from the semi-discontinuous DNA replication model, was not observed on S. cerevisiae chromosomes. Even around two highly efficient replication origins, ARS522 and ARS416, the ratios of Okazaki fragments on both strands were inconsistent with the semi-discontinuous DNA replication model. Our study supported the discontinuous DNA replication model. Besides, we also observed that Okazaki fragments were overpresented in the transcribed regions in S. cerevisiae mitochondrial genome, which indicated the interplay between transcription and DNA replication. Examination of the distribution of Okazaki fragments in Saccharomyces cerevisiae strain S288C.
2013-06-18 | E-GEOD-42929 | biostudies-arrayexpress
Project description:We investigated the genome-wide distribution of Okazaki fragments in the commonly used laboratory Saccharomyces cerevisiae strain S288C to study the DNA replication model adopted by the budding yeast. The method based upon lambda exonuclease digestion for purification of RNA-primed replication intermediates was first improved to be suitable for the purification of Okazaki fragments. Then, we used this improved method to purify Okazaki fragments from S288C yeast cells, followed by Illumina sequencing. We found that the expected asymmetric distribution of Okazaki fragments around confirmed replication origins, which was derived from the semi-discontinuous DNA replication model, was not observed on S. cerevisiae chromosomes. Even around two highly efficient replication origins, ARS522 and ARS416, the ratios of Okazaki fragments on both strands were inconsistent with the semi-discontinuous DNA replication model. Our study supported the discontinuous DNA replication model. Besides, we also observed that Okazaki fragments were overpresented in the transcribed regions in S. cerevisiae mitochondrial genome, which indicated the interplay between transcription and DNA replication.
2013-06-18 | GSE42929 | GEO
Project description:Given sustainability and scalability concerns of using sugar feedstocks for microbial bioproduction of bulk chemicals, widening the feedstock range for microbial cell factories is of high interest. Methanol is a one-carbon alcohol that stands out as an alternative feedstock for the bioproduction of chemicals, as it is electron-rich, water-miscible and can be produced from several renewable resources. Bioconversion of methanol into products under thermophilic conditions (>50 °C) could be highly advantageous for industrial biotechnology. Although progress is being made with natural, thermophilic methylotrophic microorganisms, they are not yet optimal for bioproduction and establishing alternative thermophilic methylotrophic bioproduction platforms can widen possibilities. Hence, we set out to implement methanol assimilation in the emerging thermophilic model organism Parageobacillus thermoglucosidasius. We engineered P. thermoglucosidasius to be strictly dependent for its growth on methanol assimilation via the core of the highly efficient ribulose monophosphate (RuMP) cycle, while co-assimilating ribose. Surprisingly, this did not require heterologous expression of RuMP enzymes. Instead, by laboratory evolution we awakened latent, native enzyme activities to form the core of the RuMP cycle. We obtained fast methylotrophic growth in which ∼17 % of biomass was strictly obtained from methanol. This work lays the foundation for developing a versatile thermophilic bioproduction platform based on renewable methanol.
2025-06-16 | PXD058329 | Pride
Project description:We study the genetics, including microarray karyotyping using comparative genomic hybridization, to explore global changes in the genomic DNA of seven S. cerevisiae strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNVs) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media. Seven S. cerevisiae strains were obtained from natural environments and different fermentation processes. The S. cerevisiae strain S288C was used as a control for microarray hybridizations. All experiments were performed using duplicate arrays, and Cy5-dCTP and Cy3-dCTP dye-swap assays were performed to reduce dye-specific bias.
2013-12-15 | E-GEOD-46165 | biostudies-arrayexpress
Project description:Thermotolerance development of robust Saccharomyces cerevisiae is necessary to enhance enzyme activity of cellulase, lower cooling costs, and reduce cell harm from the bad-distributed heat transfer in large-scale fermentation. The process-based studies of adaptive evolution have been well documented, but it remains unknown for the underlying molecular mechanism of the improved thermotolerance and the facilitated ethanol fermentability derived from adaptive evolution. Here, a robust thermotolerant S. cerevisiae Z100 was obtained with significantly improved ethanol fermentability under the stress of high temperature (50 oC) after 91 days’ adaptive evolution. RNA sequencing showed that adaptive evolution and its derived thermotolerance contributed to the unique gene transcriptional landscapes of the evolved strain. An interesting phenomenon was that the gene transcriptional signals of carbon metabolism were strengthened not at 50 oC but at 30 oC in S. cerevisiae Z100, and thus suggested that the improved thermotolerance led to the enhanced ethanol fermentability at 30 oC. The deeply repressed gene transcriptional expression indicated ribosome would be another key thermotolerant mechanism for the evolved strain. This study would provide a robust thermotolerant S. cerevisiae for bioethanol production and an important clue for future synthetic biology to thermotolerance engineering of fermentation strains.
2021-08-20 | GSE182342 | GEO