Dataset Information

Phosphorylation Mapping of Atg13 in Response to Atg1 Activity and Rapamycin Treatment in Budding Yeast

ABSTRACT: We performed phosphorylation site mapping on of budding yeast Atg13 applying a quantitative mass spectrometry-based proteomics approach based on stable isotope labeling with amino acids in cell culture (SILAC). We determined changes in the Atg13 phosphorylation pattern in response of inhibition of kinase Atg1 and starvation conditions (using rapamycin), respectively. To do so, Atg13 was tandem purified via a histidine-biotin (HB) tag from cells growing at the respective experimental condition. Different stimulus-dependent PTM profiles of Atg13 have been identified.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Wolfgang Reiter

LAB HEAD: Claudine Kraft

PROVIDER: PXD028461 | Pride | 2024-01-20

REPOSITORIES: Pride

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Publications

Decoding the function of Atg13 phosphorylation reveals a role of Atg11 in bulk autophagy initiation.

Bhattacharya Anuradha A Torggler Raffaela R Reiter Wolfgang W Romanov Natalie N Licheva Mariya M Ciftci Akif A Mari Muriel M Kolb Lena L Kaiser Dominik D Reggiori Fulvio F Ammerer Gustav G Hollenstein David M DM Kraft Claudine C

EMBO reports 20240117 2

Autophagy is initiated by the assembly of multiple autophagy-related proteins that form the phagophore assembly site where autophagosomes are formed. Atg13 is essential early in this process, and a hub of extensive phosphorylation. How these multiple phosphorylations contribute to autophagy initiation, however, is not well understood. Here we comprehensively analyze the role of phosphorylation events on Atg13 during nutrient-rich conditions and nitrogen starvation. We identify and functionally c ...[more]

PMID: 38233718

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Project description:Action of alcohol on synaptic mRNA in the amygdala of mice Chronic alcohol consumption induces changes in gene expression, causing persistent long-term neuro-adaptations and the remodeling of synaptic structures. These alcohol-induced synaptic changes may rely specifically on the local translation of mRNAs in the synaptic compartments of the cell. We profiled the transcriptome from synaptoneurosomes (SN) and paired total homogenates (TH) of amygdala to analyze the synaptic adaptations induced by chronic voluntary alcohol consumption in mice. In the SN both the number of alcohol-responsive mRNAs and the magnitude of fold-change were greater than in the TH. Accordingly, the SN detected many genes with coordinated patterns of expression producing a highly connected mRNA network in gene co-expression analysis. The greater sensitivity of the SN preparation allowed for improved cell-type specificity analysis, revealing an up-regulation of alcohol-responsive astrocytic and microglial modules that correlated with alcohol consumption. Alcohol was found to induce changes in the SN functionally important biological pathways, including long-term potentiation, long-term potentiation depression, glutamate pathway, neuro-immune, RNA-processing and translational machineries and provided overlap with changes seen in human alcoholic brain. Transposable elements were responsive to alcohol and found in the down-regulated neuronal mRNA module, which may underlie some of the coordinated gene expression changes associated with alcohol. We provide evidence that enrichment of synaptic components reveals a more intricate network of coordinated gene expression. Increased resolution captures the molecular effects of synaptic manipulations and provides an improved technique for identifying therapeutic targets for alcohol abuse. Synaptoneurosomes (SN) and Paired total homogenates (TH) were prepared from the same homogenate. 42 microarrays were used in total for the alcohol-control analysis (8 alcohol treated mice and 13 controls), 21 SN and 21 paired TH. 2 TH (control) samples were found outliers and were removed from the analysis. For the SN vs. TH analysis, the 2 TH samples found outliers were removed with the 2 paired SN samples.

Dataset Information

Phosphorylation Mapping of Atg13 in Response to Atg1 Activity and Rapamycin Treatment in Budding Yeast

Publications

Decoding the function of Atg13 phosphorylation reveals a role of Atg11 in bulk autophagy initiation.

Similar Datasets

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