Name: Mitochondrial retrograde signaling contributes to metabolic differentiation in yeast colonies - Proteomics of BY4742, BY-rtg1, BY-mks1, BY-rtg1mks1 and BY-rtg2mks1.
Keywords: Mitochondrial retrograde signaling

Dataset Information

Mitochondrial retrograde signaling contributes to metabolic differentiation in yeast colonies - Proteomics of BY4742, BY-rtg1, BY-mks1, BY-rtg1mks1 and BY-rtg2mks1.

ABSTRACT: The associated files are mass spec data ........ of proteins from colonies of Saccharomyces cerevisiae BY4742, BY-rtg1, BY-mks1, BY-rtg1mks1 and BY-rtg2mks1 strains.

INSTRUMENT(S): Orbitrap Fusion

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

SUBMITTER: Karel Harant

LAB HEAD: Zdena Palková

PROVIDER: PXD026077 | Pride | 2022-02-17

REPOSITORIES: Pride

ACCESS DATA

Publications

Mitochondrial Retrograde Signaling Contributes to Metabolic Differentiation in Yeast Colonies.

Plocek Vítězslav V Fadrhonc Kristýna K Maršíková Jana J Váchová Libuše L Pokorná Alexandra A Hlaváček Otakar O Wilkinson Derek D Palková Zdena Z

International journal of molecular sciences 20210525 11

During development of yeast colonies, various cell subpopulations form, which differ in their properties and specifically localize within the structure. Three branches of mitochondrial retrograde (RTG) signaling play a role in colony development and differentiation, each of them activating the production of specific markers in different cell types. Here, aiming to identify proteins and processes controlled by the RTG pathway, we analyzed proteomes of individual cell subpopulations from colonies ...[more]

PMID: 34070491

Similar Datasets

Project description:Human multipotent stromal cells readily form single-cell-derived colonies when plated at clonal densities. However, the colonies are heterogeneous because cells from a colony form new colonies that vary in size and differentiation potential when replated at clonal densities. The experiments here tested the hypothesis that cells in the inner regions of colonies are partially differentiated, but the differentiation is reversible. Cells were separately isolated from the dense inner (IN) regions and less-dense outer regions (OUT) of single-cell-derived colonies. Cells were then compared by assays of their transcriptomes and proteins, and for clonogenicity and differentiation. IN cells expressed fewer cell-cycle genes and higher levels of genes for extracellular matrix than the OUT cells. When transferred to differentiation medium, differentiation of the colonies occurred primarily in the IN regions. However, the IN cells were indistinguishable from OUT cells when replated at clonal densities and assayed for rates of propagation and clonogenicity. Also, colonies formed by IN cells were similar to colonies formed by OUT cells because they had distinct IN and OUT regions. Cultures of IN and OUT cells remained indistinguishable through multiple passages (30-75 population doublings), and both cells formed colonies that were looser and less dense as they were expanded. The results demonstrated that cells in the IN region of single-cell-derived colonies are partially differentiated, but the differentiation can be reversed by replating the cells at clonal densities. Experiment Overall Design: In this study heterogeneity of human multipotent stromal cells in single-cell-derived colonies was examined. Cells were grown as colonies on slides for 12 days and cells from inside (IN) and outside (OUT) of colonies were isolated with laser capture microdissection. Cells from two colonies were pooled for each sample. This study consists of 3 biological replicates for each colony region (3 for IN and 3 for OUT). All 6 samples were run on Affymetrix microarrays after amplification and labeling using Nugen Ovation technology.

Project description:Genetically identical cells are known to differ in many physiological parameters such as growth rate and drug tolerance, but the source of such heterogeneity is often insufficiently understood. Exchange interactions between metabolite producing and consuming cells are believed to be one possible cause, but detecting metabolically divergent subpopulations remains technically challenging. We developed a proteomics-based technology, termed differential isotope labelling by amino acids (DILAC), which monitors amino acid incorporation into peptides with multiple occurrences of the same amino acid. DILAC is used to differentiate producer and consumer cells of a particular amino acid within an isogenic cell population. We applied DILAC to young, morphologically undifferentiated yeast colonies and reveal that they contain sub-populations of lysine producers and consumers which emerge due to nutrient gradients. DILAC can deconvolute the proteome of subpopulations from bulk measurements which indicated an in situ cross feeding situation where fast growing cells ferment and provide the slower growing, respiring cells with ethanol as substrate. Finally, by combining DILAC with FACS, we show that the metabolic states that differ between isogenic cells, confer resistance to the antifungal drug amphotericin B. Overall, this novel and broadly applicable methodological approach captures previously unnoticed metabolic heterogeneity, providing experimental evidence for the role of metabolic specialisation and cross-feeding interactions as a source of phenotypic heterogeneity in isogenic cell populations. This submission contains 8 raw files as well as the following additional files relating to Dataset 3: DIA-NN_pipeline_PRIDE.pipeline - The DIA-NN pipeline file containing all the settings to run the analysis. In the first step, a modified spectral library with the required fixed and variable isotope labels was predicted. In the second step, the data files are analysed; 20210225_yeastspeclib.tsv.speclib - The original spectral library; sSwath_yeastspeclib_C13K.predicted.speclib - The isotope-modified library; sSwath_yeastspeclib_C13K.predicted.ExcludeFromAssay.speclib.tsv - The isotope-modified library with unsuitable fragments excluded using the ExcludeFromAssay column; modify_library.ipynb - Jupyter notebook used to add ExcludeFromAssay column to library to filter suitable fragments for quantification; 20220428_Ex8_rerun_ExcludeFromAssay.tsv - The main DIA-NN report; hit_calling_PRIDE.ipynb - Jupyter notebook containing code for hit calling. This submission contains an additional 7 raw files as well as the following additional files relating to the spike-in experiment shown in Extended View 4 E-G.

Dataset Information

Mitochondrial retrograde signaling contributes to metabolic differentiation in yeast colonies - Proteomics of BY4742, BY-rtg1, BY-mks1, BY-rtg1mks1 and BY-rtg2mks1.

Publications

Mitochondrial Retrograde Signaling Contributes to Metabolic Differentiation in Yeast Colonies.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure