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1.
Int J Mol Sci ; 25(2)2024 Jan 08.
Article in English | MEDLINE | ID: mdl-38255855

ABSTRACT

Sterols exert a profound influence on numerous cellular processes, playing a crucial role in both health and disease. However, comprehending the effects of sterol dysfunction on cellular physiology is challenging. Consequently, numerous processes affected by impaired sterol biosynthesis still elude our complete understanding. In this study, we made use of yeast strains that produce cholesterol instead of ergosterol and investigated the cellular response mechanisms on the transcriptome as well as the lipid level. The exchange of ergosterol for cholesterol caused the downregulation of phosphatidylethanolamine and phosphatidylserine and upregulation of phosphatidylinositol and phosphatidylcholine biosynthesis. Additionally, a shift towards polyunsaturated fatty acids was observed. While the sphingolipid levels dropped, the total amounts of sterols and triacylglycerol increased, which resulted in 1.7-fold enlarged lipid droplets in cholesterol-producing yeast cells. In addition to internal storage, cholesterol and its precursors were excreted into the culture supernatant, most likely by the action of ABC transporters Snq2, Pdr12 and Pdr15. Overall, our results demonstrate that, similarly to mammalian cells, the production of non-native sterols and sterol precursors causes lipotoxicity in K. phaffii, mainly due to upregulated sterol biosynthesis, and they highlight the different survival and stress response mechanisms on multiple, integrative levels.


Subject(s)
Phytosterols , Sterols , Animals , Humans , Saccharomyces cerevisiae , Ergosterol , Cholesterol , Mammals
2.
Mol Cell Proteomics ; 20: 100095, 2021.
Article in English | MEDLINE | ID: mdl-33992777

ABSTRACT

Cancer cells undergo complex metabolic adaptations to survive and thrive in challenging environments. This is particularly prominent for solid tumors, where cells in the core of the tumor are under severe hypoxia and nutrient deprivation. However, such conditions are often not recapitulated in the typical 2D in vitro cancer models, where oxygen as well as nutrient exposure is quite uniform. The aim of this study was to investigate the role of a key neutral lipid hydrolase, namely adipose triglyceride lipase (ATGL), in cancer cells that are exposed to more tumor-like conditions. To that end, we cultured lung cancer cells lacking ATGL as multicellular spheroids in 3D and subjected them to comprehensive proteomics analysis and metabolic phenotyping. Proteomics data are available via ProteomeXchange with identifier PXD021105. As a result, we report that loss of ATGL enhanced growth of spheroids and facilitated their adaptation to hypoxia, by increasing the influx of glucose and endorsing a pro-Warburg effect. This was followed by changes in lipid metabolism and an increase in protein production. Interestingly, the observed phenotype was also recapitulated in an even more "in vivo like" setup, when cancer spheroids were grown on chick chorioallantoic membrane, but not when cells were cultured as a 2D monolayer. In addition, we demonstrate that according to the publicly available cancer databases, an inverse relation between ATGL expression and higher glucose dependence can be observed. In conclusion, we provide indications that ATGL is involved in regulation of glucose metabolism of cancer cells when grown in 3D (mimicking solid tumors) and as such could be an important factor of the treatment outcome for some cancer types. Finally, we also ratify the need for alternative cell culture models, as the majority of phenotypes observed in 3D and spheroids grown on chick chorioallantoic membrane were not observed in 2D cell culture.


Subject(s)
Acyltransferases/metabolism , Carcinoma, Non-Small-Cell Lung/metabolism , Lung Neoplasms/metabolism , Acyltransferases/genetics , Animals , Chick Embryo , Chorioallantoic Membrane , Glucose/metabolism , Humans , Spheroids, Cellular , Tumor Cells, Cultured
3.
Clin Proteomics ; 19(1): 46, 2022 Dec 17.
Article in English | MEDLINE | ID: mdl-36526981

ABSTRACT

The outbreak of a novel coronavirus (SARS-CoV-2) in 2019 led to a worldwide pandemic, which remains an integral part of our lives to this day. Coronavirus disease (COVID-19) is a flu like condition, often accompanied by high fever and respiratory distress. In some cases, conjointly with other co-morbidities, COVID-19 can become severe, leading to lung arrest and even death. Although well-known from a clinical standpoint, the mechanistic understanding of lethal COVID-19 is still rudimentary. Studying the pathology and changes on a molecular level associated with the resulting COVID-19 disease is impeded by the highly infectious nature of the virus and the concomitant sampling challenges. We were able to procure COVID-19 post-mortem lung tissue specimens by our collaboration with the BSL-3 laboratory of the Biobanking and BioMolecular resources Research Infrastructure Austria which we subjected to state-of-the-art quantitative proteomic analysis to better understand the pulmonary manifestations of lethal COVID-19. Lung tissue samples from age-matched non-COVID-19 patients who died within the same period were used as controls. Samples were subjected to parallel accumulation-serial fragmentation combined with data-independent acquisition (diaPASEF) on a timsTOF Pro and obtained raw data was processed using DIA-NN software. Here we report that terminal COVID-19 patients display an increase in inflammation, acute immune response and blood clot formation (with concomitant triggering of fibrinolysis). Furthermore, we describe that COVID-19 diseased lungs undergo severe extracellular matrix restructuring, which was corroborated on the histopathological level. However, although undergoing an injury, diseased lungs seem to have impaired proliferative and tissue repair signalling, with several key kinase-mediated signalling pathways being less active. This might provide a mechanistic link to post-acute sequelae of COVID-19 (PASC; "Long COVID"). Overall, we emphasize the importance of histopathological patient stratification when interpreting molecular COVID-19 data.

4.
Mol Cell Proteomics ; 19(12): 2104-2115, 2020 12.
Article in English | MEDLINE | ID: mdl-33023980

ABSTRACT

Despite the crucial function of the small intestine in nutrient uptake our understanding of the molecular events underlying the digestive function is still rudimentary. Recent studies demonstrated that enterocytes do not direct the entire dietary triacylglycerol toward immediate chylomicron synthesis. Especially after high-fat challenges, parts of the resynthesized triacylglycerol are packaged into cytosolic lipid droplets for transient storage in the endothelial layer of the small intestine. The reason for this temporary storage of triacylglycerol is not completely understood. To utilize lipids from cytosolic lipid droplets for chylomicron synthesis in the endoplasmic reticulum, stored triacylglycerol has to be hydrolyzed either by cytosolic lipolysis or lipophagy. Interestingly, triacylglycerol storage and chylomicron secretion rates are unevenly distributed along the small intestine, with the proximal jejunum exhibiting the highest intermittent storage capacity. We hypothesize that correlating hydrolytic enzyme activities with the reported distribution of triacylglycerol storage and chylomicron secretion in different sections of the small intestine is a promising strategy to determine key enzymes in triacylglycerol remobilization. We employed a serine hydrolase specific activity-based labeling approach in combination with quantitative proteomics to identify and rank hydrolases based on their relative activity in 11 sections of the small intestine. Moreover, we identified several clusters of enzymes showing similar activity distribution along the small intestine. Merging our activity-based results with substrate specificity and subcellular localization known from previous studies, carboxylesterase 2e and arylacetamide deacetylase emerge as promising candidates for triacylglycerol mobilization from cytosolic lipid droplets in enterocytes.


Subject(s)
Intestine, Small/enzymology , Lipase/metabolism , Proteomics , Animals , Hydrolases/metabolism , Male , Mice, Inbred C57BL
5.
Int J Mol Sci ; 23(6)2022 Mar 20.
Article in English | MEDLINE | ID: mdl-35328776

ABSTRACT

Non-alcoholic fatty liver disease is a pathology with a hard-to-detect onset and is estimated to be present in a quarter of the adult human population. To improve our understanding of the development of non-alcoholic fatty liver disease, we treated a human hepatoma cell line model, HepG2, with increasing concentrations of common fatty acids, namely myristic, palmitic and oleic acid. To reproduce more physiologically representative conditions, we also included combinations of these fatty acids and monitored the cellular response with an in-depth proteomics approach and imaging techniques. The two saturated fatty acids initially presented a similar phenotype of a dose-dependent decrease in growth rates and impaired lipid droplet formation. Detailed analysis revealed that the drop in the growth rates was due to delayed cell-cycle progression following myristic acid treatment, whereas palmitic acid led to cellular apoptosis. In contrast, oleic acid, as well as saturated fatty acid mixtures with oleic acid, led to a dose-dependent increase in lipid droplet volume without adverse impacts on cell growth. Comparing the effects of harmful single-fatty-acid treatments and the well-tolerated fatty acid mixes on the cellular proteome, we were able to differentiate between fatty-acid-specific cellular responses and likely common lipotoxic denominators.


Subject(s)
Non-alcoholic Fatty Liver Disease , Fatty Acids/metabolism , Fatty Acids, Nonesterified/metabolism , Fatty Acids, Nonesterified/pharmacology , Hepatocytes/metabolism , Humans , Non-alcoholic Fatty Liver Disease/metabolism , Oleic Acid/metabolism , Oleic Acid/pharmacology , Palmitic Acid/metabolism , Palmitic Acid/pharmacology , Proteome/metabolism
6.
Allergy ; 76(6): 1743-1753, 2021 06.
Article in English | MEDLINE | ID: mdl-33301602

ABSTRACT

BACKGROUND: In addition to known allergens, other proteins in pollen can aid the development of an immune response in allergic individuals. The contribution of the "unknown" protein allergens is apparent in phylogenetically related species where, despite of high homology of the lead allergens, the degree of allergenic potential can vary greatly. The aim of this study was to identify other potentially allergenic proteins in pollen of three common and highly related allergenic tree species: birch (Betula pendula), hazel (Corylus avellana) and alder (Alnus glutinosa). METHODS: For that purpose, we carried out a comprehensive, comparative proteomic screening of the pollen from the three species. In order to maximize protein recovery and coverage, different protein extraction and isolation strategies during sample preparation were employed. RESULTS: As a result, we report 2500-3000 identified proteins per each of the pollen species. Identified proteins were further used for a number of annotation steps, providing insight into differential distribution of peptidases, peptidase inhibitors and other potential allergenic proteins across the three species. Moreover, we carried out functional enrichment analyses that, interestingly, corroborated high species similarity in spite of their relatively distinct protein profiles. CONCLUSION: We provide to our knowledge first insight into proteomes of two very important allergenic pollen types, hazel and alder, where not even transcriptomics data are available, and compared them to birch. Datasets from this study can be readily used as protein databases and as such serve as basis for further functional studies.


Subject(s)
Alnus , Corylus , Allergens , Betula , Humans , Pollen , Proteomics , Trees
7.
Mol Cell Proteomics ; 18(8): 1511-1525, 2019 08.
Article in English | MEDLINE | ID: mdl-31123107

ABSTRACT

Reinke's edema is a smoking-associated, benign, mostly bilateral lesion of the vocal folds leading to difficulties in breathing and voice problems. Pronounced histological changes such as damaged microvessels or immune cell infiltration have been described in the vocal fold connective tissue, the lamina propria Thus, vocal fold fibroblasts, the main cell type of the lamina propria, have been postulated to play a critical role in disease mediation. Yet information about the pathophysiology is still scarce and treatment is only surgical, i.e. symptomatic. To explore the pathophysiology of Reinke's edema, we exposed near-primary human vocal fold fibroblasts to medium conditioned with cigarette smoke extract for 24 h as well as 4 days followed by quantitative mass spectrometry.Proteomic analyses after 24 h revealed that cigarette smoke increased proteins previously described to be involved in oxidative stress responses in other contexts. Correspondingly, gene sets linked to metabolism of xenobiotics and reactive oxygen species were significantly enriched among cigarette smoke-induced proteins. Among the proteins most downregulated by cigarette smoke, we identified fibrillar collagens COL1A1 and COL1A2; this reduction was validated by complementary methods. Further, we found a significant increase of UDP-glucose 6-dehydrogenase, generating a building block for biosynthesis of hyaluronan, another crucial component of the vocal fold lamina propria In line with this result, hyaluronan levels were significantly increased because of cigarette smoke exposure. Long term treatment of 4 days did not lead to significant changes.The current findings corroborate previous studies but also reveal new insights in possible disease mechanisms of Reinke's edema. We postulate that changes in the composition of the vocal folds' extracellular matrix -reduction of collagen fibrils, increase of hyaluronan- may lead to the clinical findings. This might ease the identification of better, disease-specific treatment options.


Subject(s)
Cigarette Smoking , Edema/metabolism , Fibroblasts/metabolism , Laryngeal Diseases/metabolism , Smoke , Vocal Cords/metabolism , Cells, Cultured , Humans , Proteomics
8.
Int J Mol Sci ; 22(23)2021 Nov 26.
Article in English | MEDLINE | ID: mdl-34884585

ABSTRACT

Hepatic stellate cells (HSC) are the major cellular drivers of liver fibrosis. Upon liver inflammation caused by a broad range of insults including non-alcoholic fatty liver, HSC transform from a quiescent into a proliferating, fibrotic phenotype. Although much is known about the pathophysiology of this process, exact cellular processes which occur in HSC and enable this transformation remain yet to be elucidated. In order to investigate this HSC transformation, we employed a simple, yet reliable model of HSC activation via an increase in growth medium serum concentration (serum activation). For that purpose, immortalized human LX-2 HSC were exposed to either 1% or 10% fetal bovine serum (FBS). Resulting quiescent (1% FBS) and activated (10% FBS) LX-2 cells were then subjected to in-depth mass spectrometry-based proteomics analysis as well as comprehensive phenotyping. Protein network analysis of activated LX-2 cells revealed an increase in the production of ribosomal proteins and proteins related to cell cycle control and migration, resulting in higher proliferation and faster migration phenotypes. Interestingly, we also observed a decrease in the expression of cholesterol and fatty acid biosynthesis proteins in accordance with a concomitant loss of cytosolic lipid droplets during activation. Overall, this work provides an update on HSC activation characteristics using contemporary proteomic and bioinformatic analyses and presents an accessible model for HSC activation. Data are available via ProteomeXchange with identifier PXD029121.


Subject(s)
Hepatic Stellate Cells/metabolism , Proteome/analysis , Proteome/metabolism , Serum Albumin, Bovine/pharmacology , Animals , Cattle , Cell Movement , Cell Proliferation , Hepatic Stellate Cells/drug effects , Humans , Proteome/drug effects
9.
Int J Mol Sci ; 22(4)2021 Feb 11.
Article in English | MEDLINE | ID: mdl-33670142

ABSTRACT

Oxidative stress contributes to detrimental functional decline of the myocardium, leading to the impairment of the antioxidative defense, dysregulation of redox signaling, and protein damage. In order to precisely dissect the changes of the myocardial redox state correlated with oxidative stress and heart failure, we subjected left-ventricular tissue specimens collected from control or failing human hearts to comprehensive mass spectrometry-based redox and quantitative proteomics, as well as glutathione status analyses. As a result, we report that failing hearts have lower glutathione to glutathione disulfide ratios and increased oxidation of a number of different proteins, including constituents of the contractile machinery as well as glycolytic enzymes. Furthermore, quantitative proteomics of failing hearts revealed a higher abundance of proteins responsible for extracellular matrix remodeling and reduced abundance of several ion transporters, corroborating contractile impairment. Similar effects were recapitulated by an in vitro cell culture model under a controlled oxygen atmosphere. Together, this study provides to our knowledge the most comprehensive report integrating analyses of protein abundance and global and peptide-level redox state in end-stage failing human hearts as well as oxygen-dependent redox and global proteome profiles of cultured human cardiomyocytes.


Subject(s)
Gene Expression Profiling , Heart Failure/metabolism , Heart Ventricles/metabolism , Mass Spectrometry , Muscle Proteins/metabolism , Myocardium/metabolism , Aged , Female , Humans , Male , Middle Aged
10.
J Nutr ; 150(10): 2707-2715, 2020 10 12.
Article in English | MEDLINE | ID: mdl-32710763

ABSTRACT

BACKGROUND: In the settings of primary and secondary prevention for coronary artery disease (CAD), a crucial role is played by some key molecules involved in triglyceride (TG) metabolism, such as ApoCIII. Fatty acid (FA) intake is well recognized as a main determinant of plasma lipids, including plasma TG concentration. OBJECTIVES: The aim was to investigate the possible relations between the intakes of different FAs, estimated by their plasma concentrations, and circulating amounts of ApoCIII. METHODS: Plasma samples were obtained from 1370 subjects with or without angiographically demonstrated CAD (mean ± SD age: 60.6 ± 11.0 y; males: 75.8%; BMI: 25.9 ± 4.6 kg/m2; CAD: 73.3%). Plasma lipid, ApoCIII, and FA concentrations were measured. Data were analyzed by regression models adjusted for FAs and other potential confounders, such as sex, age, BMI, diabetes, smoking, and lipid-lowering therapies. The in vitro effects of FAs were tested by incubating HepG2 hepatoma cells with increasing concentrations of selected FAs, and the mRNA and protein contents in the cells were quantified by real-time RT-PCR and LC-MS/MS analyses. RESULTS: Among all the analyzed FAs, myristic acid (14:0) showed the most robust correlations with both TGs (R = 0.441, P = 2.6 × 10-66) and ApoCIII (R = 0.327, P = 1.1 × 10-31). By multiple regression analysis, myristic acid was the best predictor of both plasma TG and ApoCIII variability. Plasma TG and ApoCIII concentrations increased progressively at increasing concentrations of myristic acid, independently of CAD diagnosis and gender. Consistent with these data, in the in vitro experiments, an ∼2-fold increase in the expression levels of the ApoCIII mRNA and protein was observed after incubation with 250 µM myristic acid. A weaker effect (∼30% increase) was observed for palmitic acid, whereas incubation with oleic acid did not affect ApoCIII protein or gene expression. CONCLUSIONS: Plasma myristic acid is associated with increased ApoCIII concentrations in cardiovascular patients. In vitro experiments indicated that myristic acid stimulates ApoCIII expression in HepG2 cells.


Subject(s)
Apolipoprotein C-III/blood , Cardiovascular Diseases/blood , Myristic Acid/blood , Aged , Gene Expression Regulation/drug effects , Hep G2 Cells , Hepatocytes/drug effects , Hepatocytes/metabolism , Humans , Male , Middle Aged , Myristic Acid/pharmacology , RNA, Messenger/genetics , RNA, Messenger/metabolism
11.
Biochim Biophys Acta Mol Cell Res ; 1865(9): 1211-1229, 2018 09.
Article in English | MEDLINE | ID: mdl-29909287

ABSTRACT

The quinazoline based drug prazosin (PRZ) is a potent inducer of apoptosis in human cancer cells. We recently reported that PRZ enters cells via endocytosis and induces tubulation of the endolysosomal system. In a proteomics approach aimed at identifying potential membrane proteins with binding affinity to quinazolines, we detected the oncoprotein CD98hc. We confirmed shuttling of CD98hc towards lysosomes and upregulation of CD98hc expression in PRZ treated cells. Gene knockout (KO) experiments revealed that endocytosis of PRZ still occurs in the absence of CD98hc - suggesting that PRZ does not enter the cell via CD98hc but misroutes the protein towards tubular lysosomes. Lysosomal tubulation interfered with completion of cytokinesis and provoked endoreplication. CD98hc KO cells showed reduced endoreplication capacity and lower sensitivity towards PRZ induced apoptosis than wild type cells. Thus, loss of CD98hc does not affect endocytosis of PRZ and lysosomal tubulation, but the ability for endoreplication and survival of cells. Furthermore, we found that glutamine, lysomototropic agents - namely chloroquine and NH4Cl - as well as inhibition of v-ATPase, interfere with the intracellular transport of CD98hc. In summary, our study further emphasizes lysosomes as target organelles to inhibit proliferation and to induce cell death in cancer. Most importantly, we demonstrate for the first time that the intracellular trafficking of CD98hc can be modulated by small molecules. Since CD98hc is considered as a potential drug target in several types of human malignancies, our study possesses translational significance suggesting, that old drugs are able to act on a novel target.


Subject(s)
Fusion Regulatory Protein 1, Heavy Chain/genetics , Fusion Regulatory Protein 1, Heavy Chain/metabolism , Lysosomes/drug effects , Neoplasms/metabolism , Prazosin/pharmacology , Cell Survival/drug effects , Cytokinesis/drug effects , Endocytosis/drug effects , Gene Expression Regulation, Neoplastic/drug effects , Gene Knockout Techniques , HEK293 Cells , Humans , K562 Cells , Lysosomes/metabolism , Neoplasms/drug therapy , Neoplasms/genetics , Protein Transport/drug effects , Up-Regulation
12.
Expert Rev Proteomics ; 16(8): 681-693, 2019 08.
Article in English | MEDLINE | ID: mdl-31361162

ABSTRACT

Introduction: Development of specific biomarkers aiding early diagnosis of heart failure is an ongoing challenge. Biomarkers commonly used in clinical routine usually act as readouts of an already existing acute condition rather than disease initiation. Functional decline of cardiac muscle is greatly aggravated by increased oxidative stress and damage of proteins. Oxidative post-translational modifications occur already at early stages of tissue damage and are thus regarded as potential up-coming disease markers. Areas covered: Clinical practice regarding commonly used biomarkers for heart disease is briefly summarized. The types of oxidative post-translational modification in cardiac pathologies are discussed with a special focus on available quantitative techniques and characteristics of individual modifications with regard to their stability and analytical accessibility. As irreversible oxidative modifications trigger protein degradation pathways or cause protein aggregation, both influencing biomarker abundance, a chapter is dedicated to their regulation in the heart.


Subject(s)
Heart Diseases/metabolism , Heart Failure/metabolism , Animals , Humans , Oxidation-Reduction , Oxidative Stress/physiology , Protein Aggregation, Pathological/metabolism , Protein Processing, Post-Translational
13.
J Proteome Res ; 17(4): 1415-1425, 2018 04 06.
Article in English | MEDLINE | ID: mdl-29457907

ABSTRACT

Adipose triglyceride lipase (ATGL) catalyzes the rate limiting step in triacylglycerol breakdown in adipocytes but is expressed in most tissues. The enzyme was shown to be lost in many human tumors, and its loss may play a role in early stages of cancer development. Here, we report that loss of ATGL supports a more-aggressive cancer phenotype in a model system in which ATGL was deleted in A549 lung cancer cells by CRISPR/Cas9. We observed that loss of ATGL led to triacylglycerol accumulation in lipid droplets and higher levels of cellular phospholipid and bioactive lipid species (lyso- and ether-phospholipids). Label-free quantitative proteomics revealed elevated expression of the pro-oncogene SRC kinase in ATGL depleted cells, which was also found on mRNA level and confirmed on protein level by Western blot. Consistently, higher expression of phosphorylated (active) SRC (Y416 phospho-SRC) was observed in ATGL-KO cells. Cells depleted of ATGL migrated faster, which was dependent on SRC kinase activity. We propose that loss of ATGL may thus increase cancer aggressiveness by activation of pro-oncogenic signaling via SRC kinase and increased levels of bioactive lipids.


Subject(s)
Lipase/deficiency , Lung Neoplasms/pathology , Triglycerides/metabolism , A549 Cells , Cell Movement/drug effects , Gene Deletion , Humans , Lipase/genetics , Lipid Metabolism , Phenotype , Proteomics , Signal Transduction/drug effects , src-Family Kinases/analysis , src-Family Kinases/metabolism , src-Family Kinases/pharmacology
14.
Anal Chem ; 90(12): 7349-7356, 2018 06 19.
Article in English | MEDLINE | ID: mdl-29792680

ABSTRACT

Folate cofactors play a key role in one-carbon metabolism. Analysis of individual folate species is hampered by the low chemical stability and high interconvertibility of folates, which can lead to severe experimental bias. Here, we present a complete workflow that employs simultaneous extraction and stabilization of folates by derivatization. We perform reductive methylation employing stable isotope labeled reagents to retain information on the position and redox state of one-carbon units as well as the redox state of the pteridine ring. The derivatives are analyzed by a targeted LC(HILIC)-MS/MS method without the need for deconjugation, thereby also preserving the glutamation state of folates. The presented method does not only improve analyte coverage and sensitivity as compared to other published methods, it also greatly simplifies sample handling and storage. Finally, we report differences in the response of bacterial and mammalian systems to pharmacological inhibition of dihydrofolate reductase.


Subject(s)
Chromatography, Liquid/methods , Folic Acid/analysis , Tandem Mass Spectrometry/methods , Workflow , Animals , Bacterial Proteins , Carbon , Folic Acid Antagonists , Hep G2 Cells , Humans , Isotope Labeling , Mammals , Methods , Methylation , Oxidation-Reduction , Pteroylpolyglutamic Acids/analysis , Tetrahydrofolate Dehydrogenase/drug effects
15.
Biochim Biophys Acta ; 1861(5): 462-70, 2016 May.
Article in English | MEDLINE | ID: mdl-26869448

ABSTRACT

Monoglyceride lipases (MGLs) are a group of α/ß-hydrolases that catalyze the hydrolysis of monoglycerides (MGs) into free fatty acids and glycerol. This reaction serves different physiological functions, namely in the last step of phospholipid and triglyceride degradation, in mammalian endocannabinoid and arachidonic acid metabolism, and in detoxification processes in microbes. Previous crystal structures of MGLs from humans and bacteria revealed conformational plasticity in the cap region of this protein and gave insight into substrate binding. In this study, we present the structure of a MGL from Saccharomyces cerevisiae called Yju3p in its free form and in complex with a covalently bound substrate analog mimicking the tetrahedral intermediate of MG hydrolysis. These structures reveal a high conservation of the overall shape of the MGL cap region and also provide evidence for conformational changes in the cap of Yju3p. The complex structure reveals that, despite the high structural similarity, Yju3p seems to have an additional opening to the substrate binding pocket at a different position compared to human and bacterial MGL. Substrate specificities towards MGs with saturated and unsaturated alkyl chains of different lengths were tested and revealed highest activity towards MG containing a C18:1 fatty acid.


Subject(s)
Monoacylglycerol Lipases/chemistry , Monoglycerides/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Binding Sites , Catalysis , Cloning, Molecular , Crystallization , Hydrolysis , Molecular Dynamics Simulation , Monoacylglycerol Lipases/genetics , Monoacylglycerol Lipases/metabolism , Monoglycerides/metabolism , Mutagenesis, Site-Directed , Mutation , Protein Binding , Protein Conformation , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Structure-Activity Relationship , Substrate Specificity
16.
Anal Chem ; 89(18): 9611-9615, 2017 09 19.
Article in English | MEDLINE | ID: mdl-28845970

ABSTRACT

High-resolution mass spectrometry has become a key technology in life sciences. Since it is often unfeasible to find pairs of analytes with an appropriate mass difference to actually quantify the resolution experimentally, resolution is usually calculated from the shape of a single mass peak. In this study we show that the commonly employed strategy yields a poor measure of true resolution since it does not account for interactions that take place between ions of very similar mass and might be further distorted by signal processing effects. We present a straightforward and easily adaptable method to create a ladder of mass pairs to experimentally quantify actual mass resolution over a wide m/z range, compare the experimental resolution to the single peak based calculated resolution, and demonstrate the applicability of mass resolution ladders to study interactions of similar ions in various types of widely used mass spectrometers.

17.
Appl Microbiol Biotechnol ; 101(6): 2291-2303, 2017 Mar.
Article in English | MEDLINE | ID: mdl-27872998

ABSTRACT

A novel esterase, PpEst, that hydrolyses the co-aromatic-aliphatic polyester poly(1,4-butylene adipate-co-terephthalate) (PBAT) was identified by proteomic screening of the Pseudomonas pseudoalcaligenes secretome. PpEst was induced by the presence of PBAT in the growth media and had predicted arylesterase (EC 3.1.1.2) activity. PpEst showed polyesterase activity on both whole and milled PBAT film releasing terephthalic acid and 4-(4-hydroxybutoxycarbonyl)benzoic acid while end product inhibition by 4-(4-hydroxybutoxycarbonyl)benzoic acid was observed. Modelling of an aromatic polyester mimicking oligomer into the PpEst active site indicated that the binding pocket could be big enough to accommodate large polymers. This is the first report of a PBAT degrading enzyme being identified by proteomic screening and shows that this approach can contribute to the discovery of new polymer hydrolysing enzymes. Moreover, these results indicate that arylesterases could be an interesting enzyme class for identifications of polyesterases.


Subject(s)
Bacterial Proteins/chemistry , Biodegradable Plastics/metabolism , Carboxylic Ester Hydrolases/chemistry , Polyesters/metabolism , Pseudomonas pseudoalcaligenes/enzymology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Biodegradable Plastics/chemistry , Carboxylic Ester Hydrolases/genetics , Carboxylic Ester Hydrolases/metabolism , Catalytic Domain , Gene Expression , Models, Molecular , Phthalic Acids/chemistry , Phthalic Acids/metabolism , Polyesters/chemistry , Protein Binding , Proteomics , Pseudomonas pseudoalcaligenes/genetics
18.
J Proteome Res ; 15(4): 1222-9, 2016 Apr 01.
Article in English | MEDLINE | ID: mdl-26938934

ABSTRACT

Chemically modified trypsin is a standard reagent in proteomics experiments but is usually not considered in database searches. Modification of trypsin is supposed to protect the protease against autolysis and the resulting loss of activity. Here, we show that modified trypsin is still subject to self-digestion, and, as a result, modified trypsin-derived peptides are present in standard digests. We depict that these peptides commonly lead to false-positive assignments even if native trypsin is considered in the database. Moreover, we present an easily implementable method to include modified trypsin in the database search with a minimal increase in search time and search space while efficiently avoiding these false-positive hits.


Subject(s)
Artifacts , Data Interpretation, Statistical , Membrane Proteins/analysis , Neoplasm Proteins/analysis , Nerve Tissue Proteins/analysis , Peptide Fragments/analysis , Saccharomyces cerevisiae Proteins/analysis , Trypsin/chemistry , Amino Acid Sequence , Animals , Brain Chemistry , Breast Neoplasms/chemistry , Cell Line , Chromatography, Liquid , Databases, Protein , Humans , Membrane Proteins/chemistry , Mice , Neoplasm Proteins/chemistry , Nerve Tissue Proteins/chemistry , Protein Structure, Secondary , Proteolysis , Proteomics/methods , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Tandem Mass Spectrometry
19.
Diabetologia ; 59(8): 1743-52, 2016 08.
Article in English | MEDLINE | ID: mdl-27153842

ABSTRACT

AIMS/HYPOTHESIS: Lysosomal acid lipase (LAL) hydrolyses cholesteryl esters and triacylglycerols (TG) within lysosomes to mobilise NEFA and cholesterol. Since LAL-deficient (Lal (-/-) ) mice suffer from progressive loss of adipose tissue and severe accumulation of lipids in hepatic lysosomes, we hypothesised that LAL deficiency triggers alternative energy pathway(s). METHODS: We studied metabolic adaptations in Lal (-/-) mice. RESULTS: Despite loss of adipose tissue, Lal (-/-) mice show enhanced glucose clearance during insulin and glucose tolerance tests and have increased uptake of [(3)H]2-deoxy-D-glucose into skeletal muscle compared with wild-type mice. In agreement, fasted Lal (-/-) mice exhibit reduced glucose and glycogen levels in skeletal muscle. We observed 84% decreased plasma leptin levels and significantly reduced hepatic ATP, glucose, glycogen and glutamine concentrations in fed Lal (-/-) mice. Markedly reduced hepatic acyl-CoA concentrations decrease the expression of peroxisome proliferator-activated receptor α (PPARα) target genes. However, treatment of Lal (-/-) mice with the PPARα agonist fenofibrate further decreased plasma TG (and hepatic glucose and glycogen) concentrations in Lal (-/-) mice. Depletion of hepatic nuclear factor 4α and forkhead box protein a2 in fasted Lal (-/-) mice might be responsible for reduced expression of microsomal TG transfer protein, defective VLDL synthesis and drastically reduced plasma TG levels. CONCLUSIONS/INTERPRETATION: Our findings indicate that neither activation nor inactivation of PPARα per se but rather the availability of hepatic acyl-CoA concentrations regulates VLDL synthesis and subsequent metabolic adaptations in Lal (-/-) mice. We conclude that decreased plasma VLDL production enhances glucose uptake into skeletal muscle to compensate for the lack of energy supply.


Subject(s)
Cholesterol, VLDL/metabolism , Insulin Resistance/physiology , Sterol Esterase/metabolism , Animals , Cholesterol, VLDL/genetics , Female , Glucose/metabolism , Insulin Resistance/genetics , Lipolysis/genetics , Lipolysis/physiology , Liver/metabolism , Lysosomes/metabolism , Male , Mice , Sterol Esterase/deficiency , Sterol Esterase/genetics , Triglycerides/metabolism
20.
J Lipid Res ; 56(1): 109-21, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25421061

ABSTRACT

CGI-58/ABHD5 coactivates adipose triglyceride lipase (ATGL). In adipocytes, CGI-58 binds to perilipin 1A on lipid droplets under basal conditions, preventing interaction with ATGL. Upon activation of protein kinase A (PKA), perilipin 1A is phosphorylated and CGI-58 rapidly disperses into the cytoplasm, enabling lipase coactivation. Because the amino acid sequence of murine CGI-58 has a predicted PKA consensus sequence of RKYS(239)S(240), we hypothesized that phosphorylation of CGI-58 is involved in this process. We show that Ser239 of murine CGI-58 is a substrate for PKA using phosphoamino acid analysis, MS, and immuno-blotting approaches to study phosphorylation of recombinant CGI-58 and endogenous CGI-58 of adipose tissue. Phosphorylation of CGI-58 neither increased nor impaired coactivation of ATGL in vitro. Moreover, Ser239 was not required for CGI-58 function to increase triacylglycerol turnover in human neutral lipid storage disorder fibroblasts that lack endogenous CGI-58. Both CGI-58 and S239A/S240A-mutated CGI-58 localized to perilipin 1A-coated lipid droplets in cells. When PKA was activated, WT CGI-58 dispersed into the cytoplasm, whereas substantial S239A/S240A-mutated CGI-58 remained on lipid droplets. Perilipin phosphorylation also contributed to CGI-58 dispersion. PKA-mediated phosphorylation of CGI-58 is required for dispersion of CGI-58 from perilipin 1A-coated lipid droplets, thereby increasing CGI-58 availability for ATGL coactivation.


Subject(s)
1-Acylglycerol-3-Phosphate O-Acyltransferase/chemistry , 1-Acylglycerol-3-Phosphate O-Acyltransferase/metabolism , Cyclic AMP-Dependent Protein Kinases/metabolism , Intracellular Space/metabolism , Serine/metabolism , Adipocytes/cytology , Adipocytes/drug effects , Adipocytes/metabolism , Amino Acid Sequence , Animals , COS Cells , Carrier Proteins/metabolism , Chlorocebus aethiops , Colforsin/pharmacology , Gene Expression Regulation/drug effects , Humans , Intracellular Space/drug effects , Lipase/metabolism , Male , Mice , Molecular Sequence Data , Perilipin-1 , Phosphoproteins/metabolism , Phosphorylation/drug effects , Protein Binding/drug effects , Protein Transport/drug effects , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism
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