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ABSTRACT: RNA-seq raw data of wt and Atg9-ko yeast during nitrogen starvation induced autophagy

PROVIDER: PRJNA513224 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8402030_1.fastq.gz	Fastqsanger.gz
	SRR8402030_2.fastq.gz	Fastqsanger.gz
	SRR8402031_1.fastq.gz	Fastqsanger.gz
	SRR8402031_2.fastq.gz	Fastqsanger.gz
	SRR8402026_1.fastq.gz	Fastqsanger.gz

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Project description:RNA-seq raw data of WT, Atg1-KO and Atg1-KD yeast during nitrogen starvation induced autophagy

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Specific features of the transcriptomic response to nitrogen starvation in methylotrophic yeast Komagataella phaffi

Project description:Non-conventional methylotrophic yeast Komagataella phaffii is an important production host in biotechnology and an emerging model organism. In this work, we studied K. phaffii response to nitrogen starvation during cultivation in media with methanol as the sole carbon source. The results were compared with well-established model yeast Saccharomyces cerevisiae. Some of the observed effects of nitrogen starvation in K. phaffii were similar to those in S. cerevisiae, despite this yeast does not have metabolic pathway for methanol utilization. The effects include activation of autophagy, transport and catabolism of nitrogen-containing compounds, interconversions of amino acids, and biosynthesis of fatty acids. K. phaffii cells also demonstrated specific response to nitrogen starvation including suppression of genes involved in methanol metabolism and other peroxisomal processes and activation of purine catabolism genes.

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AI-based multi-omic integration uncovers Atg1 interactome and substratome in yeast autophagy

Project description:As a core Autophagy-related (Atg) protein during yeast autophagy, Atg1 interacts with numerous other proteins, and its kinase activity facilitates to phosphorylate various substrates. How Atg1-interacting partners and substrates synergistically orchestrate autophagy remains to be further dissected. In this study, we conducted a transcriptomic, proteomic and phosphoproteomic profiling of Atg1-dependent molecular landscapes during nitrogen starvation-triggered autophagy.

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Project description:In order to asses yeast EC1118® strain expression changes during wine alcoholic fermentation triggered by various nutrient starvations, this experiment describes the gene expression under micronutrient starvations that lead to yeast cell death (oleic acid starvation, ergosterol starvation, pantothenic acid starvation and nicotinic starvation) or allow the maintenance of yeast viability (nitrogen starvation).

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Transcriptional regulation by Pho23 modulates the frequency of autophagosome formation.

Project description:Autophagy as a conserved degradation and recycling machinery is important in normal development and physiology, and defects in this process are linked to many kinds of disease. Because too much or too little autophagy can be detrimental, the process must be tightly regulated both temporally and in magnitude. The transcriptional induction and repression of the autophagy-related (ATG) genes is one crucial aspect of this regulation, but the transcriptional regulators that modulate autophagy are not well characterized. In this study, we identified Pho23 as a master transcriptional repressor for autophagy, with transcriptome profiling revealing that ATG9 is one of the key target genes. Physiological studies with a PHO23 null mutant, or with strains expressing modulated levels of Atg9, demonstrate a critical role of this protein as a regulator of autophagosome formation frequency; Atg9 protein levels correlate with the number of autophagosomes generated upon autophagy induction, and the level of autophagy activity. WT yeast and pho23 deletion mutants were grown under nutrient rich or nitrogen starvation conditions; gene expression was quantified across these 4 samples.

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Saccharomyces cerevisiae - Quorum Sensing

Project description:Comparison of 3 yeast strains grown under nitrogen starvation, nitrogen rich conditions, with and without quorum sensing molecule 2-phenylethanol

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Project description:In Saccharomyces cerevisiae, Atg9 is an important AuTophaGy-related (Atg) protein, plays critical roles in regulating macroautophagy/autophagy, and physically interacts with hundreds of proteins. How Atg9 interacting partners are synergistically orchestrated in autophagy are unclear. Here, we conducted a transcriptomic and proteomic profiling of Atg9-dependent molecular landscapes during nitrogen starvation-induced autophagy.

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Potassium starvation induces autophagy in yeast

Project description:Potassium starvation induces autophagy in yeast

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Project description:The general consensus is that the vacuolar-type H+-translocating ATPase (V-ATPase) is critical for macroautophagy/autophagy. However, there is a fundamental conundrum because follicular lymphoma-associated mutations in the V-ATPase result in lysosomal/vacuolar deacidification but elevated autophagy activity under nutrient-replete conditions and the underlying mechanisms remain mysterious. Here, working in yeast, we show that V-ATPase dysfunction activates a selective autophagy flux termed the "V-ATPase-autophagy axis". By combining transcriptomic and proteomic profiling, along with genome-wide suppressor screening approaches, we found that the V-ATPase-autophagy axis is regulated through a unique mechanism distinct from classical nitrogen starvation-induced autophagy. Tryptophan metabolism negatively regulates the V-ATPase-autophagy axis via two parallel effectors. On the one hand, it activates ribosome biogenesis, thus repressing the translation of the transcription factor Gcn4/ATF4. On the other hand, tryptophan fuels NAD+ de novo biosynthesis to inhibit autophagy. These results provide a clear explanation for the mutational activation of autophagy seen in follicular lymphoma patients.

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2023-12-15 | PXD045932 | Pride

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