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Saccharomyces cerevisiae CEN.PK113-7D

ABSTRACT: Anaerobically evolved fungi that harbor Class II dihydroorotate dehydrogenase enzymes that function independently of the respiratory chain

PROVIDER: PRJNA745202 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15616355_1.fastq.gz	Fastqsanger.gz
	SRR15616355_2.fastq.gz	Fastqsanger.gz
	SRR15616356_1.fastq.gz	Fastqsanger.gz
	SRR15616356_2.fastq.gz	Fastqsanger.gz
	SRR15616357_1.fastq.gz	Fastqsanger.gz

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Saccharomyces cerevisiae isolate:IMX2816 | breed:CEN.PK113-7D

Project description:Engineering class-B vitamin biosynthesis in Saccharomyces cerevisiae (IMX2816)

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Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D.

Project description:The haploid Saccharomyces cerevisiae strain CEN.PK113-7D is a popular model system for metabolic engineering and systems biology research. Current genome assemblies are based on short-read sequencing data scaffolded based on homology to strain S288C. However, these assemblies contain large sequence gaps, particularly in subtelomeric regions, and the assumption of perfect homology to S288C for scaffolding introduces bias. In this study, we obtained a near-complete genome assembly of CEN.PK113-7D using only Oxford Nanopore Technology's MinION sequencing platform. Fifteen of the 16 chromosomes, the mitochondrial genome and the 2-μm plasmid are assembled in single contigs and all but one chromosome starts or ends in a telomere repeat. This improved genome assembly contains 770 Kbp of added sequence containing 248 gene annotations in comparison to the previous assembly of CEN.PK113-7D. Many of these genes encode functions determining fitness in specific growth conditions and are therefore highly relevant for various industrial applications. Furthermore, we discovered a translocation between chromosomes III and VIII that caused misidentification of a MAL locus in the previous CEN.PK113-7D assembly. This study demonstrates the power of long-read sequencing by providing a high-quality reference assembly and annotation of CEN.PK113-7D and places a caveat on assumed genome stability of microorganisms.

| S-EPMC5812507 | biostudies-literature

Transcription profiling of yeast protrotophic laboratory strain CEN.PK113-7D grown under glutamine or ammonia limited conditions

Project description:The protrotophic laboratory strain CEN.PK113-7D (MAT a) was grown in laboratory fermentors with a working volume of 1 litre at dilution rate (D) of 0.20 per hour (in duplicate for each nitrogen (glutamine and ammonium) limited condition). After cultivation for few hundred generations in ammonium, samples from 2 continuous cultures were taken for array analysis. After cultivation for few hundred generations in glutamine, one evolved strain was picked and cultivated in 2 biological replicate chemostats until steady state was reached, and samples for array analysis were collected. All collected cell samples were cooled below 2 degree C within ten seconds by mixing 40% sample and 60% crushed ice.

2008-06-01 | E-MEXP-1498 | biostudies-arrayexpress

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D.

Project description:Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction. Assembly of the reads derived from all three technologies resulted in complete sequences for all 16 yeast chromosomes, as well as the mitochondrial chromosome, in one step. Further, we identified three types of DNA methylation (5mC, 4mC and 6mA). Comparison between the reference strain S288C and strain CEN.PK113-7D identified chromosomal rearrangements against a background of similar gene content between the two strains. We identified full-length transcripts through ONT direct RNA sequencing technology. This allows for the identification of transcriptional landscapes, including untranslated regions (UTRs) (5' UTR and 3' UTR) as well as differential gene expression quantification. About 91% of the predicted transcripts could be consistently detected across biological replicates grown either on glucose or ethanol. Direct RNA sequencing identified many polyadenylated non-coding RNAs, rRNAs, telomere-RNA, long non-coding RNA and antisense RNA. This work demonstrates a strategy to obtain complete genome sequences and transcriptional landscapes that can be applied to other eukaryal organisms.

| S-EPMC5909453 | biostudies-literature

Anaerobic growth of Saccharomyces cerevisiae CEN.PK113-7D does not depend on synthesis or supplementation of unsaturated fatty acids.

Project description:In Saccharomyces cerevisiae, acyl-coenzyme A desaturation by Ole1 requires molecular oxygen. Tween 80, a poly-ethoxylated sorbitan-oleate ester, is therefore routinely included in anaerobic growth media as a source of unsaturated fatty acids (UFAs). During optimization of protocols for anaerobic bioreactor cultivation of this yeast, we consistently observed growth of the laboratory strain S. cerevisiae CEN.PK113-7D in media that contained the anaerobic growth factor ergosterol, but lacked UFAs. To minimize oxygen contamination, additional experiments were performed in an anaerobic chamber. After anaerobic precultivation without ergosterol and Tween 80, strain CEN.PK113-7D and a congenic ole1Δ strain both grew during three consecutive batch-cultivation cycles on medium that contained ergosterol, but not Tween 80. During these three cycles, no UFAs were detected in biomass of cultures grown without Tween 80, while contents of C10 to C14 saturated fatty acids were higher than in biomass from Tween 80-supplemented cultures. In contrast to its UFA-independent anaerobic growth, aerobic growth of the ole1Δ strain strictly depended on Tween 80 supplementation. This study shows that the requirement of anaerobic cultures of S. cerevisiae for UFA supplementation is not absolute and provides a basis for further research on the effects of lipid composition on yeast viability and robustness.

| S-EPMC6750169 | biostudies-literature

Saccharomyces cerevisiae CEN.PK113-7D

Project description:Evolutionary and reverse engineering of single vitamin requirement in Saccharomyces cerevisiae CEN.PK113-7D

| PRJNA603441 | ENA

Saccharomyces cerevisiae CEN.PK113-7D

Project description:Mutations in the galactose-transporter gene GAL2 enable anaerobic growth of glucose-phosphorylation-negative, arabinose-fermenting yeast strains in the presence of glucose

| PRJNA414371 | ENA

Saccharomyces cerevisiae CEN.PK113-7D

Project description:Saccharomyces cerevisiae CEN.PK113-7D Raw sequence reads

| PRJNA354846 | ENA

Saccharomyces cerevisiae CEN.PK113-7D

Project description:Saccharomyces cerevisiae CEN.PK113-7D Genome sequencing and assembly

| PRJNA400448 | ENA

Saccharomyces cerevisiae CEN.PK113-7D

Project description:Laboratory evolution of a biotin-requiring Saccharomyces cerevisiae strain for full biotin prototrophy and identification of causal mutations (Raw sequence reads)

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