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Saccharomyces cerevisiae CEN.PK113-7D

ABSTRACT: Arginine auxotrophy by deletion of the mitochondrial selectable marker ARG8 in Saccharomyces cerevisiae can be reverted by loss-of-function mutations in UME6

PROVIDER: PRJNA906461 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22442628_1.fastq.gz	Fastqsanger.gz
	SRR22442628_2.fastq.gz	Fastqsanger.gz
	SRR22442629_1.fastq.gz	Fastqsanger.gz
	SRR22442629_2.fastq.gz	Fastqsanger.gz
	SRR22442630_1.fastq.gz	Fastqsanger.gz

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Saccharomyces cerevisiae CEN.PK113-7D

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Saccharomyces cerevisiae CEN.PK113-7D

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Saccharomyces cerevisiae strain:CEN.PK113-7D

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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.

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Transcriptome regulation in response to respiratory inhibition with antimycin A in: (a) wild type fission yeast grown in minimal media (EMM) (b) minimal media supplemented with arginine or in (c) strain with deletion of ssp1 gene.

Project description:We observed that in fission yeast respiration inhibition with drug antimycin A results in arginine auxotrophy. To get insights into transcriptional response for respiratory inhibition and attenuating role of arginine supplementation we performed microarray experiment. Yeast were growing exponentially (OD600 around 0.5) in minimal media (EMM), transcript abundance was monitored immediately prior (Time 0), and 30 and 120 minutes after addition to the media antimycin A (to the concentration 0.15 µg/ml). We performed such experiment for wild type yeast (strain 972 h-), wild type yeast grown in minimal media supplemented with arginine (to the concentration 0.2g/L), and for ssp1 deletion strain grown in minimal media. Ssp1 regulates AMPK kinase and our microarray data show that is can modulate response for respiration block. Two biological samples for each condition (EMM, EMM with arginine and ssp1 deletion) was collected. Part of all the samples were pooled and used as reference in dye swap design.

2020-03-30 | E-MTAB-8805 | biostudies-arrayexpress

RNAseq analysis of mutants in coding and non-coding transcription of phosphate genes in the yeast Saccharomyces cerevisiae.

Project description:This study addresses the effect of mutations related to sense and antisense transcription of Saccharomyces cerevisiae phosphate genes using strand-specific RNAseq. Replacement of the transcriptional terminator of PHO84 by that of CYC1 resulted, unexpectedly, in an increased antisense transcription and a strongly reduced sense transcription of PHO84. Also RNA levels of SPL2 were strongly reduced. Deletion of the PHO84 coding region did not markedly affect the expression of SPL2, suggesting that antisense transcription of PHO84 and not the Pho84 transporter affects the expression of SPL2. Deletion of the two putative binding sites for the transcriptional regulator Ume6 in the SPL2 promoter resulted in a slightly increased level of SPL2 RNA, whereas deletion of the UME6 gene resulted in a decreased level of SPL2 and PHO84 RNA. These results suggests that Ume6 is involved in the regulation of SPL2 by a mechanism different from a simple binding to the putative Ume6 binding sites.

2024-03-06 | GSE226971 | GEO

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.

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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.

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