Saccharomyces cerevisiae mitochondrial fractions by LC-MS/MS
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap Velos
ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)
SUBMITTER: 
Holger Kramer
LAB HEAD: Tobias Warnecke
PROVIDER: PXD008785 | Pride | 2018-04-09
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Uniprot_Cerevisiae_20160815.fasta | Fasta | |||
| b023p018_MSS1_TR01.raw | Raw | |||
| b023p018_MSS1_TR02.raw | Raw | |||
| b023p018_MSS2_TR01.raw | Raw | |||
| b023p018_MSS2_TR02.raw | Raw |
Items per page: 5 1 - 5 of 20 |
Publications
Normal mitochondrial function in <i>Saccharomyces cerevisiae</i> has become dependent on inefficient splicing.
Rudan Marina M Bou Dib Peter P Musa Marina M Kanunnikau Matea M Sobočanec Sandra S Rueda David D Warnecke Tobias T Kriško Anita A
eLife 20180323
Self-splicing introns are mobile elements that have invaded a number of highly conserved genes in prokaryotic and organellar genomes. Here, we show that deletion of these selfish elements from the <i>Saccharomyces cerevisiae</i> mitochondrial genome is stressful to the host. A strain without mitochondrial introns displays hallmarks of the retrograde response, with altered mitochondrial morphology, gene expression and metabolism impacting growth and lifespan. Deletion of the complete suite of mit ...[more]
Similar Datasets
Project description:Hyperhomocysteinemia (HHcy) inhibits growth and is cytotoxic to bacterial, yeast, and mammalian cells. The aim of this study was to determine the changes in proteome of the yeast induced by HHcy and map N-homocysteinylated sites. We identified 38 up- and 32-down-regulated proteins as well as 244 N-homocysteinylation sites in 98 proteins in Saccharomyces cerevisiae; with 57 sites in 34 proteins occurring in vivo. The bioinformatics analysis indicated that the N-homocysteinylated proteins were involved in a wide range of cellular functions with mostly cytosolic and ribosomal localizations. Furthermore, we discovered that lysine N-homocysteinylation sites are surrounded by neutral, hydrophobic and buried amino acid residues, and 60% of them occur within helix. The KEGG enrichment pathway analysis of these N-Hcy-proteins suggested that N-homocysteinylation disrupts metabolism of amino acids, ribosome biogenesis and glycolysis/gluconeogenesis. These findings suggest that protein N-homocysteinylation and dysregulation of cellular proteostasis affecting ribosomal proteins, biosynthesis of amino acids and changes in basic cellular pathways signaling are involved in the toxicity of HHcy in yeast. Homologous proteins are likely to be involved in HHcy toxicity in human and animal cells. We believe that the collection of N-homocysteinylation sites presented here is an important resource for future functional studies of N-homocysteinylation in yeast.
2022-02-16 | PXD019951 | Pride
Project description:The high biological potential of polyphenols encourages the search for new natural sources of and biomedical applications for these compounds. Rhododendron luteum Sweet was previously reported to contain pharmaceutically active polyphenols. The present research investigates the polyphenolic fractions in R. luteum leaves, including a determination of the free and bound phenolic acid and flavonoid contents and their anti-inflammatory and antioxidant activities. LC-ESI-MS/MS (liquid chromatography/electrospray ionization triple quadrupole mass spectrometry) analysis revealed a great abundance of free (e.g., 5-O-caffeoylquinic acid, ferulic acid, protocatechuic acid, catechin, and dihydromyricetin) and bound (e.g., caffeic acid, p-coumaric, protocatechuic acid, myricetin, quercetin) phenolics. The R. luteum samples exhibited high anti-inflammatory potential in lipoxygenase (IC50: 0.33 ± 0.01-2.96 ± 0.06 mg dry extract (DE)/mL) and hyaluronidase (IC50: 78.76 ± 2.09 - 429.07 ± 31.08 µg DE/mL) inhibition capacity assays. Some samples also had the ability to inhibit cyclooxygenase 1 (IC50: 311.8 ± 10.95 µg DE/mL) and cyclooxygenase 2 (IC50: 53.40 ± 5.07; 608.09 ± 14.78 µg DE/mL). All fractions showed excellent antioxidant activity in the Oxygen Radical Absorbance Capacity (ORAC) assay (5.76-221.81 g Trolox/g DE), ABTS•+ radical scavenging ability (0.62 ± 0.03 - 5.09 ± 0.23 g Trolox/g DE), and moderate ion (Fe2+) chelating power. This paper expands our knowledge of the phytochemistry and pharmacological activity of R. luteum polyphenols. It reveals, for the first time, the presence of dihydromyricetin, afzelin, and laricitrin in the plant material. It indicates biologically active polyphenolic fractions that should be further investigated or which could be efficiently used in pharmaceutical, cosmetic, or nutraceutical applications.
| S-EPMC8840727 | biostudies-literature
Project description:We carried out LC-MS/MS-based proteomic profiling of differential centrifugation fractions from rat inner medullary collecting duct (IMCD): 1) to provide baseline knowledge of the IMCD proteome and 2) to evaluate the utility of differential centrifugation in assessing trafficking of the water channel aquaporin-2 (AQP2). IMCD suspensions were freshly prepared from rat kidneys using standard methods. Homogenized samples were subjected to sequential centrifugations at 1,000, 4,000, 17,000, and 200,000 g. These samples, as well as the final supernatant, were subjected to LC-MS/MS analysis. Preliminary immunoblotting confirmed that the ratio of AQP2 in the 17,000-g fraction to the 200,000-g fraction underwent an increase in response to the vasopressin analog dDAVP, largely due to a reduction in the 200,000-g fraction. Immunoblotting for the major phosphorylated forms of AQP2 revealed that phosphorylated AQP2 was present in both the 17,000- and 200,000-g fractions. LC-MS/MS analysis showed that markers of "intracellular vesicles," chiefly endosomal markers, were present in both the 17,000- and the 200,000-g fractions. In contrast, plasma membrane proteins were predominantly present in the 4,000- and 17,000-g fractions. Proteins associated with several multiprotein complexes (e.g., actin-related protein 2/3 complex and proteasome complex) were virtually exclusively present in the 200,000-g fraction. Overall, we identified 656 proteins, including 189 not previously present in the IMCD database. The data show that both the 17,000- and 200,000-g fractions are highly heterogeneous and cannot be equated with "plasma membrane" and "intracellular vesicle" fractions, respectively, leading us to propose an alternative approach for use of differential centrifugation to assess vesicular trafficking to the plasma membrane.
| S-EPMC2604837 | biostudies-other
Project description:Early-onset colorectal cancer (EOCRC; age younger than 50 years) incidence has been steadily increasing over the last decades worldwide with causes unexplained. A unique molecular feature of EOCRC is that these cases harbor a greater incidence of Nodal Modulator 1 (NOMO1) somatic deletions compared with late-onset CRC. Yet the mechanisms of NOMO1 in early-onset colorectal carcinogenesis are currently unknown. Here we show that 50% of heterozygous NOMO1 deleted–EOCRCs presented pathogenic mutations in this gene, suggesting that NOMO1 can be inactivated by deletion or mutation in EOCRC. To study its role in EOCRC, CRISPR/cas9 technology was used to generate NOMO1 knockout HCT-116 (EOCRC) and HS-5 (bone marrow) cell lines. Loss of NOMO1 in these cell lines did not perturb Nodal pathway signaling. Results from expression microarray, RNA sequencing and protein expression analysis by LC-IMS/MS revealed that NOMO1 inactivation deregulates other signaling pathways independent of the Nodal pathway such as epithelial-mesenchymal transition. Importantly, NOMO1 inactivation increased the migration capacity of CRC cells. Additionally, a gut-specific conditional KO mouse model of NOMO1 revealed no subsequent tumor development in mice. Overall, these findings suggest that NOMO1 could not be a driver of early-onset colorectal carcinogenesis, but its loss promotes an increased migration capacity of CRC cells. Further study is warranted to explore other signaling pathways deregulated by the loss of NOMO1 that may play a relevant role in the pathogenesis of the disease.
2022-10-15 | PXD033636 | Pride
Project description:In vitro cell culture studies are common in cancer research field, and reliable biomimetic 3D models are needed to ensure physiological relevance. In this manuscript, we hypothesized that decellularized xenograft tumors can serve as an optimal 3D substrate to generate a top-down approach for in vitro tumor modeling. Methods: Multiple tumor cell lines were xenografted and the formed solid tumors were recovered for their decellularization by several techniques and further characterization by histology and proteomics techniques. Selected decellularized tumor xenograft samples were seeded with human triple negative breast cancer (TNBC)c ells and cell behavior was compared among them and with other control 2D and 3D cell culture methods. Results: A soft treatment using Freeze-EDTA-DNAse allows proper decellularization of xenografted tumor samples. Interestingly, proteomic data show that samples decellularized from TMBC xenograft models had different extracellular matrix (ECM) composition compared to the rest of xenograft tumors tested. The in vitro re-cellularization of decellularized ECM (dECM) yields tumor-type specific cell-behavior in TNBC context. Conclusions: Data indicate that dECM derived from xenograft tumors is a feasible substrate for re-seeding purposes, thereby promoting tumor-type specific cell behavior. These data serve as a proof-of-concept for further potential generation of patient-specific in vitro research models.
2022-09-12 | PXD034597 | Pride
Project description:Investigation of utilization possibilities of natural sources has been an important area for research. Tyrosinase inhibitory activity plays a key role in food and medicine industry. Strawberry tree (Arbutus unedo), a widely distributed plant among Mediterranean countries, possess fruits and leaves with rich bioactive phytochemicals, especially polyphenolic compounds. In this study, we aimed to investigate the antityrosinase activity of the fruit and leaf extracts of the plant, and to determine the phenolic compounds that contribute to the antityrosinase activity. In this regard, we evaluated the effect of solvent composition on the extraction of phenolic compounds from A. unedo and on its antityrosinase activity using a simplex centroid design approach, and used chromatographic and LC-MS/MS techniques. The leaf extracts prepared using EtOH:water (50:50) provided higher TPC (456.39 mg GAE/g extract) and acetone:EtOH:water (33:33:33) provided higher TFC (56.15 mg QE/g extract) values than of fruit extracts. LC-MS/MS analysis revealed 23 phenolic/flavonoid compounds in leaf extracts (L1-8), and major metabolites were detected as quercitrin, quinic acid, catechin, tannic acid, isoquercitrin, gallic acid, and ellagic acid. Among the leaf extracts, L3 (aceton:water, 50:50) exhibited 72.01% tyrosinase inhibition at 500 μg/mL. After fractionation studies guided by antityrosinase activity, its subfraction L3-Fr2 exhibited 40.06% inhibition at 50 μg/mL concentration (IC50: 146 ± 7.75 μg/mL), and catechin (113.19 mg/g), tannic acid (53.14 mg/g), ellagic acid (22.14 mg/g), gallic acid (10.27 mg/g), and epicatechin gallate (8.65 mg/g) were determined as major metabolites. Its subfraction L3-Fr2-sub7 exhibited better antityrosinase activity (IC50: 206.23 ± 9.87 μg/mL), and quantitative analysis results revealed the presence of tannic acid (127.40 mg/g), gallic acid (13.96 mg/g), ellagic acid (7.66 mg/g), quercetin-3-O-glucuronide (5.06 mg/g), and quinic acid (3.2 mg/g) as major metabolites, and correlation analysis showed that ellagic acid and quinic acid were positively correlated with antityrosinase activity.
| S-EPMC11210468 | biostudies-literature
Project description:The probability of synaptic vesicle (SV) fusion in response to an action potential, termed vesicular release probability (Pr), is a stochastic but tightly regulated process. SNARE proteins are the molecular executors of SV fusion and therefore, key modulators of Pr. The non-canonical SNARE VAMP4 is a cargo for activity-dependent bulk endocytosis (ADBE), a major SV retrieval mode operating during intense neuronal activity. Using optical imaging in primary neuronal cultures and slice electrophysiology from wild-type and VAMP4 knockout mice, we reveal that modulation of VAMP4 copy number on SVs is an important mechanism to regulate Pr. The control of VAMP4 copy number is determined by its clearance from axons via the endolysosomal system after its retrieval by ADBE. This activity-dependent regulatory mechanism enables synapses to 1) adapt their Pr dynamically to changing input and 2) couple regulation of synaptic strength to neuronal proteostasis.
2021-03-11 | PXD021437 | Pride
Project description:FACT mediates cohesin function on chromatin Cohesin is a key regulator of genome architecture with roles in sister chromatid cohesion and the organisation of higher-order structures during interphase and mitosis. The recruitment and mobility of cohesin complexes on DNA are restricted by nucleosomes. Here we show that cohesin role in chromosome organization requires the histone chaperone FACT. Depletion of FACT in metaphase cells affects cohesin stability on chromatin reducing its accumulation at pericentric regions and binding on chromosome arms. Using Hi-C, we show that cohesin-dependent TAD (Topological Associated Domains)-like structures in G1 and metaphase chromosomes are disrupted in the absence of FACT. Surprisingly, sister chromatid cohesion is intact in FACT-depleted cells, although chromosome segregation failure is observed. Our results uncover a role for FACT in genome organisation by facilitating cohesin dependent compartmentalization of chromosomes into loop domains.
2019-10-03 | PXD014896 | Pride
Project description:For the first time, trapped ion mobility spectrometry (TIMS) in tandem with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is applied to the analysis of the low energy water accommodated fraction (WAF) of a crude oil as a function of the exposure to light. The TIMS-FT-ICR MS analysis provided, in addition to the heteroatom series identification, new insights into the WAF isomeric complexity (e.g., [m/z; chemical formula; collision cross section] data sets) for a better evaluation of the degree of chemical and structural photoinduced transformations. Inspection of the [m/z; chemical formula; collision cross section] data sets shows that the WAF composition changes as a function of the exposure to light in the first 115 h by initial photosolubilization of HC components and their photo-oxidation up to O4-5 of mainly high double bond equivalence species (DBE > 9). The addition of high resolution TIMS (resolving power of 90-220) to ultrahigh resolution FT-ICR MS (resolving power over 400k) permitted the identification of a larger number of molecular components in a single analysis (e.g., over 47k using TIMS-MS compared to 12k by MS alone), with instances of over 6-fold increase in the number of molecular features per nominal mass due to the WAF isomeric complexity. This work represents a stepping stone toward a better understanding of the WAF components and highlights the need for better experimental and theoretical approaches to characterize the WAF structural diversity.
| S-EPMC5661887 | biostudies-literature
Project description:The human N-terminal acetyltransferase E (NatE) including its associated NatA co-translationally acetylates the N-terminus of about 40-60% of the proteome to mediate diverse biological processes including protein half-life, localization and protein interaction. In eukaryotes, the NatE complex contains the NAA50 catalytic subunit with substrate specificity for N-terminal methionine acetylation and NatA, which facilitates ribosomal targeting of the complex for co-translational activity. NatA, contains NAA10 catalytic and NAA15 auxiliary subunits, and forms a complex with a protein with intrinsic NAA10 inhibitory activity, HYPK. The molecular basis for how the human NAA10 and NAA50 catalytic subunits within NatE complex coordinate function and how HYPK regulates NatE activity is unknown. Here, we characterize the biochemical interplay between the human NAA10 and NAA50 catalytic subunits of NatE and its regulation by HYPK and correlate this to the cryo-EM structures of the human NatE and NatE/HYPK complexes. We show that NAA50 and HYPK exhibit negative cooperative binding to NatA in vitro and in human cells, by inducing NAA15 shifts in opposing directions. NAA50 and HYPK each contributes to NAA10 activity inhibition through structural alteration of the NAA10 substrate binding site. NatE is about 8-fold more active than NAA50, likely due to a reduced entropic cost for substrate binding through NatA tethering, but is inhibited by HYPK through structural alteration of the NatE substrate binding site. Taken together, these studies reveal the molecular basis for coordinated N-terminal acetylation by the NAA10 and NAA50 catalytic subunits of NatE and its modulation by HYPK.
2020-03-13 | PXD017031 | Pride