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Richards S, Palmer D, Cawley A, Wainscott M, Keledjian J. Enhanced analysis of equine plasma for the presence of recombinant human erythropoietin - Implementation of an improved workflow. Drug Test Anal 2024. [PMID: 39097987 DOI: 10.1002/dta.3785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024]
Abstract
An improved screening workflow and a robust capillary flow LC-MS confirmatory method for the detection of recombinant human erythropoietin (rHuEPO) has been implemented to increase the sensitivity of rHuEPO detection and to reduce the number of suspect samples committed to confirmatory testing. The influence of repeated dosing of epoetin-β on the detection window of rHuEPO in equine plasma was assessed using the optimised method. Samples were initially assessed using an economical R&D Human EPO Duo-Set ELISA Development System. Samples indicating a result greater than the batch baseline were analysed using the complementary R&D Human EPO Quantikine IVD ELISA kit. All samples recording an abnormal screening result were subjected to confirmatory analysis. Confirmation of rHuEPO in plasma (≥2.5 ml) in the range of 4-13 mIU/ml (n = 6) was achieved using immunoaffinity enrichment, tryptic digestion, and capillary flow LC-MS/MS. Four horses were administered a single dose of epoetin-β (10,000 IU) via the subcutaneous and intravenous routes, on two occasions, seven days apart. The excretion profile was rapid with epoetin-β detection times of 48 to 72 h following each administration, with no appreciable difference observed between the two routes of administration. This workflow has been shown as an effective anti-doping strategy related to rHuEPO misuse and supports the use of out-of-competition testing of horses in the 2 to 3-day period prior to race-day.
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Affiliation(s)
- Stacey Richards
- Australian Racing Forensic Laboratory, Racing NSW, Sydney, NSW, Australia
| | - David Palmer
- New Zealand Racing Laboratory Services Ltd, Avondale, Auckland, New Zealand
| | - Adam Cawley
- Australian Racing Forensic Laboratory, Racing NSW, Sydney, NSW, Australia
| | | | - John Keledjian
- Australian Racing Forensic Laboratory, Racing NSW, Sydney, NSW, Australia
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2
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Krishnarjuna B, Sharma G, Hiiuk VM, Struppe J, Nagorny P, Ivanova MI, Ramamoorthy A. Nanodisc Reconstitution and Characterization of Amyloid-β Precursor Protein C99. Anal Chem 2024; 96:9362-9369. [PMID: 38826107 DOI: 10.1021/acs.analchem.3c05727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimer's disease (AD). Since the fragmentation of the membrane-bound APP that results in the production of amyloid-β peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable and suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in the native Escherichia. coli membrane environment is demonstrated.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Gaurav Sharma
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Volodymyr M Hiiuk
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Pavel Nagorny
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Magdalena I Ivanova
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida 32310, United States
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3
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Krishnarjuna B, Sharma G, Hiiuk VM, Struppe J, Nagorny P, Ivanova MI, Ramamoorthy A. Nanodisc reconstitution and characterization of amyloid-β precursor protein C99. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.21.590446. [PMID: 38659865 PMCID: PMC11042261 DOI: 10.1101/2024.04.21.590446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimer's disease. Since the fragmentation of the membrane-bound APP that results in the production of amyloid-beta peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable/suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in native E. coli membrane environment is demonstrated.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Gaurav Sharma
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Volodymyr M Hiiuk
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Pavel Nagorny
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Magdalena I Ivanova
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL 32310, United States
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, United States
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4
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Smeriglio N, Li H, Mazli WNAB, Bendel K, Hao L. Contaminant Spot Check and Removal Assay (ContamSPOT) for Mass Spectrometry Analysis. Anal Chem 2024; 96:2574-2581. [PMID: 38291764 DOI: 10.1021/acs.analchem.3c05020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Mass spectrometry (MS) analysis is often challenged by contaminations from detergents, salts, and polymers that compromise data quality and can damage the chromatography and MS instruments. However, researchers often discover contamination issues only after they acquire the data. There is no existing contaminant assay that is sensitive enough to detect trace amounts of contaminants from a few microliters of samples prior to MS analysis. To address this crucial need in the field, we developed a sensitive, rapid, and cost-effective contaminant spot check and removal assay (ContamSPOT) to detect and quantify trace amounts of contaminants, such as detergents, salts, and other chemicals commonly used in the MS sample preparation workflow. Only 1 μL of the sample was used prior to MS injection to quantify contaminants by ContamSPOT colorimetric or fluorometric assay on a thin layer chromatography (TLC) plate. We also optimized contaminant removal methods to salvage samples with minimal loss when ContamSPOT showed a positive result. ContamSPOT was then successfully applied to evaluate commonly used bottom-up proteomic methods regarding the effectiveness of removing detergent, peptide recovery, reproducibility, and proteome coverage. We expect ContamSPOT to be widely adopted by MS laboratories as a last-step quality checkpoint prior to MS injection. We provided a practical decision tree and a step-by-step protocol with a troubleshooting guide to facilitate the use of ContamSPOT by other researchers. ContamSPOT can also provide a unique readout of sample cleanliness for developing new MS-based sample preparation methods in the future.
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Affiliation(s)
- Noah Smeriglio
- Department of Chemistry, The George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, D.C. 20052, United States
| | - Haorong Li
- Department of Chemistry, The George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, D.C. 20052, United States
| | - Wan Nur Atiqah Binti Mazli
- Department of Chemistry, The George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, D.C. 20052, United States
| | - Katharine Bendel
- Department of Chemistry, The George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, D.C. 20052, United States
| | - Ling Hao
- Department of Chemistry, The George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, D.C. 20052, United States
- Department of Biochemistry and Molecular Medicine, The George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, D.C. 20052, United States
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5
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Mashini A, Oakley CA, Peng L, Grossman AR, Weis VM, Davy SK. Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian-dinoflagellate symbiosis. THE ISME JOURNAL 2024; 18:wrae122. [PMID: 38988135 PMCID: PMC11473927 DOI: 10.1093/ismejo/wrae122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 05/02/2024] [Accepted: 07/09/2024] [Indexed: 07/12/2024]
Abstract
Cellular mechanisms responsible for the regulation of nutrient exchange, immune responses, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved, particularly with respect to the dinoflagellate symbiont. Here, we characterized proteomic changes in the native symbiont Breviolum minutum during colonization of its host sea anemone Exaiptasia diaphana ("Aiptasia"). We also compared the proteome of this native symbiont in the established symbiotic state with that of a non-native symbiont, Durusdinium trenchii. The onset of symbiosis between Aiptasia and Breviolum minutum increased the accumulation of symbiont proteins associated with the acquisition of inorganic carbon and photosynthesis, nitrogen metabolism, micro- and macronutrient starvation, suppression of host immune responses, tolerance to low pH, and management of oxidative stress. Such responses are consistent with a functional, persistent symbiosis. In contrast, D. trenchii predominantly showed elevated levels of immunosuppressive proteins, consistent with the view that this symbiont is an opportunist that forms a less beneficial, less well-integrated symbiosis with this model anemone. By adding symbiont analysis to the already known responses of the host proteome, our results provide a more holistic view of cellular processes that determine host-symbiont specificity and how differences in symbiont partners (i.e. native versus non-native symbionts) may impact the fitness of the cnidarian-dinoflagellate symbiosis.
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Affiliation(s)
- Amir Mashini
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Clinton A Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Lifeng Peng
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Arthur R Grossman
- Biosphere Sciences and Engineering, The Carnegie Institution for Science, Stanford, CA 94305, United States
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, United States
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
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6
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Srapyan S, Tran DP, Loo JA, Grintsevich EE. Mapping Molecular Interaction Interface Between Diaphanous Formin-2 and Neuron-Specific Drebrin A. J Mol Biol 2023; 435:168334. [PMID: 37898384 DOI: 10.1016/j.jmb.2023.168334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/13/2023] [Accepted: 10/23/2023] [Indexed: 10/30/2023]
Abstract
Actin cytoskeleton is critical for neuronal shape and function. Drebrin and formins are key regulators of neuronal actin networks. Neuron-specific drebrin A is highly enriched in dendritic spines (postsynaptic terminals) of mature excitatory neurons. Decreased levels of drebrin in dendritic spines is a hallmark of Alzheimer's disease, epilepsy, and other complex disorders, which calls for better understanding of its regulatory functions. Drebrin A was previously shown to inhibit actin nucleation and bundling by the diaphanous formin-2 (mDia2) - an actin nucleator that is involved in the initiation of dendritic spines. Characterization of the molecular binding interface between mDia2 and drebrin is necessary to better understand the functional consequences of this interaction and its biological relevance. Prior work suggested a multi-pronged interface between mDia2 and drebrin, which involves both N-terminal and C-terminal regions of the drebrin molecule. Here we used mass spectrometry analysis, deletion mutagenesis, and an array of synthetic peptides of neuronal drebrin A to map its formin-binding interface. The mDia2-interacting interface on drebrin was narrowed down to three highly conserved 9-16 residue sequences that were used to identify some of the key residues involved in this interaction. Deletion of the C-terminal region of drebrin greatly reduces its binding to mDia2 and the extent of its inhibition of formin-driven actin assembly. Moreover, our experiments with formins from different subfamilies showed that drebrin is a specific rather than general inhibitor of these proteins. This work contributes to a molecular level understanding of the formin-drebrin interaction and will help to unravel its biological significance.
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Affiliation(s)
- Sargis Srapyan
- Department of Chemistry and Biochemistry, California State University, Long Beach (CSULB), Long Beach, CA 90840, USA
| | - Denise P Tran
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; Sydney Mass Spectrometry, The University of Sydney (USyd), Sydney, New South Wales 2006, Australia
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Elena E Grintsevich
- Department of Chemistry and Biochemistry, California State University, Long Beach (CSULB), Long Beach, CA 90840, USA.
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7
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Maurer J, Grouzmann E, Eugster PJ. Tutorial review for peptide assays: An ounce of pre-analytics is worth a pound of cure. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1229:123904. [PMID: 37832388 DOI: 10.1016/j.jchromb.2023.123904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
The recent increase in peptidomimetic-based medications and the growing interest in peptide hormones has brought new attention to the quantification of peptides for diagnostic purposes. Indeed, the circulating concentrations of peptide hormones in the blood provide a snapshot of the state of the body and could eventually lead to detecting a particular health condition. Although extremely useful, the quantification of such molecules, preferably by liquid chromatography coupled to mass spectrometry, might be quite tricky. First, peptides are subjected to hydrolysis, oxidation, and other post-translational modifications, and, most importantly, they are substrates of specific and nonspecific proteases in biological matrixes. All these events might continue after sampling, changing the peptide hormone concentrations. Second, because they include positively and negatively charged groups and hydrophilic and hydrophobic residues, they interact with their environment; these interactions might lead to a local change in the measured concentrations. A phenomenon such as nonspecific adsorption to lab glassware or materials has often a tremendous effect on the concentration and needs to be controlled with particular care. Finally, the circulating levels of peptides might be low (pico- or femtomolar range), increasing the impact of the aforementioned effects and inducing the need for highly sensitive instruments and well-optimized methods. Thus, despite the extreme diversity of these peptides and their matrixes, there is a common challenge for all the assays: the need to keep concentrations unchanged from sampling to analysis. While significant efforts are often placed on optimizing the analysis, few studies consider in depth the impact of pre-analytical steps on the results. By working through practical examples, this solution-oriented tutorial review addresses typical pre-analytical challenges encountered during the development of a peptide assay from the standpoint of a clinical laboratory. We provide tips and tricks to avoid pitfalls as well as strategies to guide all new developments. Our ultimate goal is to increase pre-analytical awareness to ensure that newly developed peptide assays produce robust and accurate results.
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Affiliation(s)
- Jonathan Maurer
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Eric Grouzmann
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Philippe J Eugster
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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8
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Brajkovic S, Rugen N, Agius C, Berner N, Eckert S, Sakhteman A, Schwechheimer C, Kuster B. Getting Ready for Large-Scale Proteomics in Crop Plants. Nutrients 2023; 15:nu15030783. [PMID: 36771489 PMCID: PMC9921824 DOI: 10.3390/nu15030783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Plants are an indispensable cornerstone of sustainable global food supply. While immense progress has been made in decoding the genomes of crops in recent decades, the composition of their proteomes, the entirety of all expressed proteins of a species, is virtually unknown. In contrast to the model plant Arabidopsis thaliana, proteomic analyses of crop plants have often been hindered by the presence of extreme concentrations of secondary metabolites such as pigments, phenolic compounds, lipids, carbohydrates or terpenes. As a consequence, crop proteomic experiments have, thus far, required individually optimized protein extraction protocols to obtain samples of acceptable quality for downstream analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). In this article, we present a universal protein extraction protocol originally developed for gel-based experiments and combined it with an automated single-pot solid-phase-enhanced sample preparation (SP3) protocol on a liquid handling robot to prepare high-quality samples for proteomic analysis of crop plants. We also report an automated offline peptide separation protocol and optimized micro-LC-MS/MS conditions that enables the identification and quantification of ~10,000 proteins from plant tissue within 6 h of instrument time. We illustrate the utility of the workflow by analyzing the proteomes of mature tomato fruits to an unprecedented depth. The data demonstrate the robustness of the approach which we propose for use in upcoming large-scale projects that aim to map crop tissue proteomes.
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Affiliation(s)
- Sarah Brajkovic
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Nils Rugen
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
- Institute of Plant Genetics, Leibniz University Hannover, 30167 Hannover, Germany
| | - Carlos Agius
- Chair of Plant Systems Biology, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Nicola Berner
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Stephan Eckert
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Amirhossein Sakhteman
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Claus Schwechheimer
- Chair of Plant Systems Biology, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
- Correspondence:
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9
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Gangras P, Gelfanova V, Williams GD, Handelman SK, Smith RM, Debets MF. Investigating SH-SY5Y Neuroblastoma Cell Surfaceome as a Model for Neuronal-Targeted Novel Therapeutic Modalities. Int J Mol Sci 2022; 23:ijms232315062. [PMID: 36499391 PMCID: PMC9739866 DOI: 10.3390/ijms232315062] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
The SH-SY5Y neuroblastoma cells are a widely used in vitro model approximating neurons for testing the target engagement of therapeutics designed for neurodegenerative diseases and pain disorders. However, their potential as a model for receptor-mediated delivery and uptake of novel modalities, such as antibody-drug conjugates, remains understudied. Investigation of the SH-SY5Y cell surfaceome will aid in greater in vitro to in vivo correlation of delivery and uptake, thereby accelerating drug discovery. So far, the majority of studies have focused on total cell proteomics from undifferentiated and differentiated SH-SY5Y cells. While some studies have investigated the expression of specific proteins in neuroblastoma tissue, a global approach for comparison of neuroblastoma cell surfaceome to the brain and dorsal root ganglion (DRG) neurons remains uninvestigated. Furthermore, an isoform-specific evaluation of cell surface proteins expressed on neuroblastoma cells remains unexplored. In this study, we define a bioinformatic workflow for the identification of high-confidence surface proteins expressed on brain and DRG neurons using tissue proteomic and transcriptomic data. We then delineate the SH-SY5Y cell surfaceome by surface proteomics and show that it significantly overlaps with the human brain and DRG neuronal surface proteome. We find that, for 32% of common surface proteins, SH-SY5Y-specific major isoforms are alternatively spliced, maintaining their protein-coding ability, and are predicted to localize to the cell surface. Validation of these isoforms using surface proteomics confirms a SH-SY5Y-specific alternative NRCAM (neuron-glia related cell adhesion molecule) isoform, which is absent in typical brain neurons, but present in neuroblastomas, making it a receptor of interest for neuroblastoma-specific therapeutics.
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Montaser AB, Kuiri J, Natunen T, Hruška P, Potěšil D, Auriola S, Hiltunen M, Terasaki T, Lehtonen M, Jalkanen A, Huttunen KM. Enhanced drug delivery by a prodrug approach effectively relieves neuroinflammation in mice. Life Sci 2022; 310:121088. [PMID: 36257461 DOI: 10.1016/j.lfs.2022.121088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/30/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
AIMS Neuroinflammation is a prominent hallmark in several neurodegenerative diseases (NDs). Halting neuroinflammation can slow down the progression of NDs. Improving the efficacy of clinically available non-steroidal anti-inflammatory drugs (NSAIDs) is a promising approach that may lead to fast-track and effective disease-modifying therapies for NDs. Here, we aimed to utilize the L-type amino acid transporter 1 (LAT1) to improve the efficacy of salicylic acid as an example of an NSAID prodrug, for which brain uptake and intracellular localization have been reported earlier. MAIN METHODS Firstly, we confirmed the improved LAT1 utilization of the salicylic acid prodrug (SA-AA) in freshly isolated primary mouse microglial cells. Secondly, we performed behavioural rotarod, open field, and four-limb hanging tests in mice, and a whole-brain proteome analysis. KEY FINDINGS The SA-AA prodrug alleviated the lipopolysaccharide (LPS)-induced inflammation in the rotarod and hanging tests. The proteome analysis indicated decreased neuroinflammation at the molecular level. We identified 399 proteins linked to neuroinflammation out of 7416 proteins detected in the mouse brain. Among them, Gps2, Vamp8, Slc6a3, Slc18a2, Slc5a7, Rgs9, Lrrc1, Ppp1r1b, Gnal, and Adcy5/6 were associated with the drug's effects. The SA-AA prodrug attenuated the LPS-induced neuroinflammation through the regulation of critical pathways of neuroinflammation such as the cellular response to stress and transmission across chemical synapses. SIGNIFICANCE The efficacy of NSAIDs can be improved via the utilization of LAT1 and repurposed for the treatment of neuroinflammation. This improved brain delivery and microglia localisation can be applied to other inflammatory modulators to achieve effective and targeted CNS therapies.
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Affiliation(s)
- Ahmed B Montaser
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
| | - Janita Kuiri
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Teemu Natunen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Pavel Hruška
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Seppo Auriola
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Tetsuya Terasaki
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Aaro Jalkanen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Kristiina M Huttunen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
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11
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Niemiec MJ, Kapitan M, Himmel M, Döll K, Krüger T, Köllner TG, Auge I, Kage F, Alteri CJ, Mobley HL, Monsen T, Linde S, Nietzsche S, Kniemeyer O, Brakhage AA, Jacobsen ID. Augmented Enterocyte Damage During Candida albicans and Proteus mirabilis Coinfection. Front Cell Infect Microbiol 2022; 12:866416. [PMID: 35651758 PMCID: PMC9149288 DOI: 10.3389/fcimb.2022.866416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/15/2022] [Indexed: 12/24/2022] Open
Abstract
The human gut acts as the main reservoir of microbes and a relevant source of life-threatening infections, especially in immunocompromised patients. There, the opportunistic fungal pathogen Candida albicans adapts to the host environment and additionally interacts with residing bacteria. We investigated fungal-bacterial interactions by coinfecting enterocytes with the yeast Candida albicans and the Gram-negative bacterium Proteus mirabilis resulting in enhanced host cell damage. This synergistic effect was conserved across different P. mirabilis isolates and occurred also with non-albicans Candida species and C. albicans mutants defective in filamentation or candidalysin production. Using bacterial deletion mutants, we identified the P. mirabilis hemolysin HpmA to be the key effector for host cell destruction. Spatially separated coinfections demonstrated that synergism between Candida and Proteus is induced by contact, but also by soluble factors. Specifically, we identified Candida-mediated glucose consumption and farnesol production as potential triggers for Proteus virulence. In summary, our study demonstrates that coinfection of enterocytes with C. albicans and P. mirabilis can result in increased host cell damage which is mediated by bacterial virulence factors as a result of fungal niche modification via nutrient consumption and production of soluble factors. This supports the notion that certain fungal-bacterial combinations have the potential to result in enhanced virulence in niches such as the gut and might therefore promote translocation and dissemination.
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Affiliation(s)
- Maria Joanna Niemiec
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
- Center for Sepsis Control and Care, Jena, Germany
| | - Mario Kapitan
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
- Center for Sepsis Control and Care, Jena, Germany
| | - Maximilian Himmel
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Kristina Döll
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Thomas Krüger
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Tobias G. Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Isabel Auge
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Franziska Kage
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Christopher J. Alteri
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Harry L.T. Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Tor Monsen
- Department Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Susanne Linde
- Center for Electron Microscopy, University Hospital, Jena, Germany
| | - Sandor Nietzsche
- Center for Electron Microscopy, University Hospital, Jena, Germany
| | - Olaf Kniemeyer
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Axel A. Brakhage
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Ilse D. Jacobsen
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
- Center for Sepsis Control and Care, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
- *Correspondence: Ilse D. Jacobsen,
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12
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Balotf S, Wilson R, Tegg RS, Nichols DS, Wilson CR. Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions. Proteomes 2022; 10:5. [PMID: 35225985 PMCID: PMC8883913 DOI: 10.3390/proteomes10010005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/31/2022] Open
Abstract
The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant-pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state of a proteome and provide a foundation for understanding the mechanisms involved in plant-pathogen interactions. This review is intended as a primer for biologists that may be unfamiliar with the diverse range of methodology for MS-based shotgun proteomics, with a focus on techniques that have been used to investigate plant-pathogen interactions. We provide a summary of the essential steps required for shotgun proteomic studies of plants, pathogens and plant-pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Finally, we discuss how protein PTMs may directly participate in the interaction between a pathogen and its host plant.
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Affiliation(s)
- Sadegh Balotf
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Robert S. Tegg
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
| | - David S. Nichols
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Calum R. Wilson
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
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13
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Method for Identifying Galectin Ligands on Lymphocyte Membrane Glycoproteins. Methods Mol Biol 2022; 2442:215-232. [PMID: 35320529 PMCID: PMC10174696 DOI: 10.1007/978-1-0716-2055-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Glycosylation is one of the most common protein posttranslational modifications. Most human lymphocyte membrane receptors are modified by diverse glycan structures, and functional studies have indicated that a family of glycan-binding proteins, galectins, can significantly modulate lymphocyte development and function by interacting with these glycans. Several galectins have a varying degree of affinity for the N-acetyllactosamine (LacNAc) disaccharide, and some critical lymphocyte receptors can be modified by glycan structures carrying this motif. However, the site-specific glycan composition on primary lymphocyte membrane receptors in healthy individuals is largely limited. The main reason for the limitation is low abundance of available material from a single donor and compositional heterogeneity in glycan structures that can potentially modify a protein. Donor-dependent variability in N-glycan structures on CD16a isolated from primary NK cells of healthy human donors was recently reported. NK cell CD16a is glycosylated at five N-glycosylation sites, and two of the five sites are modified, almost exclusively, by N-glycans with multiple LacNAc repeats which can serve as ligands for endogenous galectins. Thus, the protocol described in this section can be utilized to identify galectin ligands at specific glycosylation sites of endogenous membrane receptor from circulating primary human lymphocytes.
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14
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Beepat SS, Davy SK, Oakley CA, Mashini A, Peng L, Bell JJ. Increased cellular detoxification, cytoskeletal activities and protein transport explain physiological stress in a lagoon sponge. J Exp Biol 2021; 224:273478. [PMID: 34661236 DOI: 10.1242/jeb.242820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/13/2021] [Indexed: 11/20/2022]
Abstract
Tropical lagoon-inhabiting organisms live in highly irradiated ecosystems and are particularly susceptible to thermal stress resulting from climate change. However, despite living close to their thermal maxima, stress response mechanisms found in these organisms are poorly understood. We used a novel physiological-proteomic approach for sponges to describe the stress response mechanisms of the lagoon-inhabiting sponge Amphimedon navalis, when exposed to elevated seawater temperatures of +2°C and +4°C relative to a 26°C ambient temperature for 4 weeks. After 4 weeks of thermal exposure, the buoyant weight of the sponge experienced a significant decline, while its pumping rates and oxygen consumption rates significantly increased. Proteome dynamics revealed 50 differentially abundant proteins in sponges exposed to elevated temperature, suggesting that shifts in the sponge proteome were potential drivers of physiological dysfunction. Thermal stress promoted an increase in detoxification proteins, such as catalase, suggesting that an excess of reactive oxygen species in sponge cells was responsible for the significant increase in oxygen consumption. Elevated temperature also disrupted cellular growth and cell proliferation, promoting the loss of sponge biomass, and the high abundance of multiple α-tubulin chain proteins also indicated an increase in cytoskeletal activities within sponge cells, which may have induced the increase in sponge pumping rate. Our results show that sustained thermal exposure in susceptible lagoonal sponges may induce significant disruption of cellular homeostasis, leading to physiological dysfunction, and that a combined physiological-proteomic approach may provide new insights into physiological functions and cellular processes occurring in sponges.
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Affiliation(s)
- Sandeep S Beepat
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Clinton A Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Amirhossein Mashini
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Lifeng Peng
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
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15
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Milkovska-Stamenova S, Wölk M, Hoffmann R. Evaluation of Sample Preparation Strategies for Human Milk and Plasma Proteomics. Molecules 2021; 26:molecules26226816. [PMID: 34833908 PMCID: PMC8618985 DOI: 10.3390/molecules26226816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Sample preparation is the most critical step in proteomics as it directly affects the subset of proteins and peptides that can be reliably identified and quantified. Although a variety of efficient and reproducible sample preparation strategies have been developed, their applicability and efficacy depends much on the biological sample. Here, three approaches were evaluated for the human milk and plasma proteomes. Protein extracts were digested either in an ultrafiltration unit (filter-aided sample preparation, FASP) or in-solution (ISD). ISD samples were desalted by solid-phase extraction prior to nRPC-ESI-MS/MS. Additionally, milk and plasma samples were directly digested by FASP without prior protein precipitation. Each strategy provided inherent advantages and disadvantages for milk and plasma. FASP appeared to be the most time efficient procedure with a low miscleavage rate when used for a biological sample aliquot, but quantitation was less reproducible. A prior protein precipitation step improved the quantitation by FASP due to significantly higher peak areas for plasma and a much better reproducibility for milk. Moreover, the miscleavage rate for milk, the identification rate for plasma, and the carbamidomethylation efficiency were improved. In contrast, ISD of both milk and plasma resulted in higher miscleavage rates and is therefore less suitable for targeted proteomics.
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Affiliation(s)
- Sanja Milkovska-Stamenova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; (M.W.); (R.H.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
- Correspondence:
| | - Michele Wölk
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; (M.W.); (R.H.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; (M.W.); (R.H.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
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16
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Park W, Son HF, Lee D, Kim IK, Kim KJ. Crystal Structure and Functional Characterization of the Bifunctional N-(5'-Phosphoribosyl)anthranilate Isomerase-indole-3-glycerol-phosphate Synthase from Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12485-12493. [PMID: 34657425 DOI: 10.1021/acs.jafc.1c05132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
L-Tryptophan is known as an aromatic amino acid and one of the essential amino acids that must be ingested through various additives or food. TrpCF is a bifunctional enzyme that has indole-glycerol-phosphate synthase (IGPS) and phosphoribosylanthranilate isomerase (PRAI) activity. In this report, we identified the crystal structure of TrpCF from Corynebacterium glutamicum (CgTrpCF) and successfully elucidated the active site by attaching rCdRP similar to the substrate and product of the TrpCF reaction. Also, we revealed that CgTrpCF shows a conformational change at the loops upon substrate binding. We analyzed amino acid sequences of the homologues of CgTrpCF, and the residues of the substrate-binding site in TrpCF were highly conserved except for some residues. These less conserved residues were replaced by site-directed mutagenesis experiments. Consequently, we obtained the CgTrpCFP294K (PRAICD/P294K) variant that has enhanced activity.
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Affiliation(s)
- Woojin Park
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyeoncheol Francis Son
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Donghoon Lee
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Il-Kwon Kim
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
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17
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Peterson AL, Siddiqui G, Sloan EK, Creek DJ. β-Adrenoceptor regulation of metabolism in U937 derived macrophages. Mol Omics 2021; 17:583-595. [PMID: 34105576 DOI: 10.1039/d1mo00057h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Macrophages have important roles in the immune system including clearing pathogens and wound healing. Metabolic phenotypes in macrophages have been associated with functional phenotypes, where pro-inflammatory macrophages have an increased rate of glycolysis and anti-inflammatory macrophages primarily use oxidative phosphorylation. β-adrenoceptor (βAR) signalling in macrophages has been implicated in disease states such as cancer, atherosclerosis and rheumatoid arthritis. The impact of βAR signalling on macrophage metabolism has not been defined. Using metabolomics and proteomics, we describe the impact of βAR signalling on macrophages treated with isoprenaline. We found that βAR signalling alters proteins involved in cytoskeletal rearrangement and redox homeostasis of the cell. We showed that βAR signalling in macrophages shifts glucose metabolism from glycolysis towards the tricarboxylic acid cycle and pentose phosphate pathways. We also show that βAR signalling perturbs purine metabolism by accumulating adenylate and guanylate pools. Taken together, these results indicate that βAR signalling shifts metabolism to support redox processes and upregulates proteins involved in cytoskeletal changes, which may contribute to βAR effects on macrophage function.
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Affiliation(s)
- Amanda L Peterson
- Drug Delivery, Disposition and Dynamics Theme, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Victoria 3052, Australia.
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18
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Ahangama Liyanage L, Harris MS, Cook GA. In Vitro Glycosylation of Membrane Proteins Using N-Glycosyltransferase. ACS OMEGA 2021; 6:12133-12142. [PMID: 34056367 PMCID: PMC8154143 DOI: 10.1021/acsomega.1c00835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Glycoproteins are post-translationally modified proteins that take part in nearly every biological process and make up a large percent of the proteome. N-Linked glycosylation can be performed by N-glycosyltransferase (NGT), which recognizes the consensus amino acid sequence, -Asn-X-Ser/Thr- (NXT), within the protein. The enzyme catalyzes glycosidic bond formation between the oligosaccharide donor, containing nucleoside phosphatase, and the amide nitrogen of the asparagine residue. The attachment of the sugar moiety can influence physiological and biological properties of the protein by affecting their folding, modulating interactions with other biomolecules, and modifying their functions at the cellular level. We are specifically interested in the properties of membrane glycoproteins, which are key components in a number of different disease states. Therefore, the use of in vitro protein glycosylation can help further evaluate the effects of the properties for these important macromolecules. In vitro studies of N-linked glycosylation were done in a stepwise fashion in a membrane-mimetic environment to confirm that the methods for glycosylating soluble proteins could be applicable to membrane proteins. Detergent and lipid systems were used since hydrophobic peptides and membrane proteins are insoluble in aqueous solvents. The stepwise method consisted of the glycosylation of a soluble 7-residue peptide, a hydrophobic WALP-NVT peptide, and a γ-sarcoglycan membrane protein, all of which contained the glycosylation site Asn-Val-Thr (NVT). Glycosylation of the samples was performed using Escherichia coli-expressed NGT from the Actinobacillus pleuropneumoniae genome, and a single sugar moiety of glucose, provided from a nucleotide-linked donor, was added to the glycosylation site. Gel electrophoresis, mass spectrometry, and NMR studies were used for the detection of glycosyltransferase activity and to show the attachment of a single glucose molecule. Our experiments demonstrated that small or large membrane proteins that contain an N-glycosylation consensus sequence can be glycosylated by NGT in membrane-mimetic environments.
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Solanský M, Mikulášek K, Zapletalová M, Petřivalský M, Chiltz A, Zdráhal Z, Leborgne-Castel N, Lochman J. The oligomeric states of elicitins affect the hypersensitive response and resistance in tobacco. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3219-3234. [PMID: 33475728 DOI: 10.1093/jxb/erab011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Successful plant defence against microbial pathogens is based on early recognition and fast activation of inducible responses. Key mechanisms include detection of microbe-associated molecular patterns by membrane-localized pattern recognition receptors that induce a basal resistance response. A well-described model of such responses to pathogens involves the interactions between Solanaceae plants and proteinaceous elicitors secreted by oomycetes, called elicitins. It has been hypothesized that the formation of oligomeric structures by elicitins could be involved in their recognition and activation of defensive transduction cascades. In this study, we tested this hypothesis using several approaches, and we observed differences in tobacco plant responses induced by the elicitin β-cryptogein (β-CRY) and its homodimer, β-CRYDIM. We also found that the C-terminal domain of elicitins of other ELI (true-elicitin) clades plays a significant role in stabilization of their oligomeric structure and restraint in the cell wall. In addition, covalently cross-linking β-CRYDIM impaired the formation of signalling complexes, thereby reducing its capacity to elicit the hypersensitive response and resistance in the host plant, with no significant changes in pathogenesis-related protein expression. By revealing the details of the effects of β-CRY dimerization on recognition and defence responses in tobacco, our results shed light on the poorly understood role of elicitins' oligomeric structures in the interactions between oomycetes and plants.
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Affiliation(s)
- Martin Solanský
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Kamil Mikulášek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Martina Zapletalová
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Marek Petřivalský
- Department of Biochemistry, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Annick Chiltz
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Nathalie Leborgne-Castel
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
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20
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Mikulášek K, Konečná H, Potěšil D, Holánková R, Havliš J, Zdráhal Z. SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS. FRONTIERS IN PLANT SCIENCE 2021; 12:635550. [PMID: 33777071 PMCID: PMC7988192 DOI: 10.3389/fpls.2021.635550] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/17/2021] [Indexed: 05/25/2023]
Abstract
Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the filter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample preparations (SP3) on carboxylated or HILIC paramagnetic beads, and protein suspension trapping method (S-Trap) were evaluated for SDS removal and protein digestion from Arabidopsis thaliana (AT) lysate. Finally, the optimized carboxylated SP3 workflow was benchmarked closely against the routine FASP. Ultimately, LC-MS/MS analyses revealed that regarding the number of identifications, number of missed cleavages, proteome coverage, repeatability, reduction of handling time, and cost per assay, the SP3 on carboxylated magnetic particles proved to be the best alternative for SDS and other contaminants removal from plant sample lysate. A robust and efficient 2-h SP3 protocol for a wide range of protein input is presented, benefiting from no need to adjust the amount of beads, binding and rinsing conditions, or digestion parameters.
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Affiliation(s)
- Kamil Mikulášek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hana Konečná
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Renata Holánková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Jan Havliš
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
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Ondrej M, Cechakova L, Fabrik I, Klimentova J, Tichy A. Lys05 - A Promising Autophagy Inhibitor in the Radiosensitization Battle: Phosphoproteomic Perspective. Cancer Genomics Proteomics 2021; 17:369-382. [PMID: 32576582 DOI: 10.21873/cgp.20196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Autophagy is a crucial factor contributing to radioresistance during radiotherapy. Although Lys05 has proven its ability to improve the results of radiotherapy through the inhibition of autophagy, molecular mechanisms of this inhibition remain elusive. We aimed to describe the molecular mechanisms involved in Lys05-induced inhibition of autophagy. MATERIALS AND METHODS Radioresistant human non-small cell lung carcinoma cells (H1299, p53-negative) and methods of quantitative phosphoproteomics were employed to define the molecular mechanisms involved in Lys05-induced inhibition of autophagy. RESULTS We confirmed that at an early stage after irradiation, autophagy was induced, whereas at a later stage after irradiation, it was inhibited. The early-stage induction of autophagy was characterized mainly by the activation of biosynthetic and metabolic processes through up- or down-regulation of the critical autophagic regulatory proteins Sequestosome-1 (SQSTM1) and proline-rich AKT1 substrate 1 (AKT1S1). The late-stage inhibition of autophagy was attributed mainly to down-regulation of Unc-51 like autophagy-activating kinase 1 (ULK1) through phosphorylation at Ser638. CONCLUSION This work contributes to emerging phosphoproteomic insights into autophagy-mediated global signaling in lung cancer cells, which might consequently facilitate the development of precision medicine therapeutics.
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Affiliation(s)
- Martin Ondrej
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, Hradec Kralove, Czech Republic
| | - Lucie Cechakova
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, Hradec Kralove, Czech Republic
| | - Ivo Fabrik
- Department of Molecular Biology and Pathology, Faculty of Military Health Sciences, University of Defense in Brno, Hradec Kralove, Czech Republic
| | - Jana Klimentova
- Department of Molecular Biology and Pathology, Faculty of Military Health Sciences, University of Defense in Brno, Hradec Kralove, Czech Republic
| | - Ales Tichy
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, Hradec Kralove, Czech Republic
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22
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Shrestha A, Mishra AK, Matoušek J, Steinbachová L, Potěšil D, Nath VS, Awasthi P, Kocábek T, Jakse J, Drábková LZ, Zdráhal Z, Honys D, Steger G. Integrated Proteo-Transcriptomic Analyses Reveal Insights into Regulation of Pollen Development Stages and Dynamics of Cellular Response to Apple Fruit Crinkle Viroid (AFCVd)-Infection in Nicotiana tabacum. Int J Mol Sci 2020; 21:E8700. [PMID: 33218043 PMCID: PMC7698868 DOI: 10.3390/ijms21228700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
Tobacco (Nicotiana tabacum) pollen is a well-suited model for studying many fundamental biological processes owing to its well-defined and distinct development stages. It is also one of the major agents involved in the transmission of infectious viroids, which is the primary mechanism of viroid pathogenicity in plants. However, some viroids are non-transmissible and may be possibly degraded or eliminated during the gradual process of pollen development maturation. The molecular details behind the response of developing pollen against the apple fruit crinkle viroid (AFCVd) infection and viroid eradication is largely unknown. In this study, we performed an integrative analysis of the transcriptome and proteome profiles to disentangle the molecular cascade of events governing the three pollen development stages: early bicellular pollen (stage 3, S3), late bicellular pollen (stage 5, S5), and 6 h-pollen tube (PT6). The integrated analysis delivered the molecular portraits of the developing pollen against AFCVd infection, including mechanistic insights into the viroid eradication during the last steps of pollen development. The isobaric tags for label-free relative quantification (iTRAQ) with digital gene expression (DGE) experiments led us to reliably identify subsets of 5321, 5286, and 6923 proteins and 64,033, 60,597, and 46,640 expressed genes in S3, S5, and PT6, respectively. In these subsets, 2234, 2108 proteins and 9207 and 14,065 mRNAs were differentially expressed in pairwise comparisons of three stages S5 vs. S3 and PT6 vs. S5 of control pollen in tobacco. Correlation analysis between the abundance of differentially expressed mRNAs (DEGs) and differentially expressed proteins (DEPs) in pairwise comparisons of three stages of pollen revealed numerous discordant changes in mRNA/protein pairs. Only a modest correlation was observed, indicative of divergent transcription, and its regulation and importance of post-transcriptional events in the determination of the fate of early and late pollen development in tobacco. The functional and enrichment analysis of correlated DEGs/DEPs revealed the activation in pathways involved in carbohydrate metabolism, amino acid metabolism, lipid metabolism, and cofactor as well as vitamin metabolism, which points to the importance of these metabolic pathways in pollen development. Furthermore, the detailed picture of AFCVd-infected correlated DEGs/DEPs was obtained in pairwise comparisons of three stages of infected pollen. The AFCVd infection caused the modulation of several genes involved in protein degradation, nuclear transport, phytohormone signaling, defense response, and phosphorylation. Intriguingly, we also identified several factors including, DNA-dependent RNA-polymerase, ribosomal protein, Argonaute (AGO) proteins, nucleotide binding proteins, and RNA exonucleases, which may plausibly involve in viroid stabilization and eradication during the last steps of pollen development. The present study provides essential insights into the transcriptional and translational dynamics of tobacco pollen, which further strengthens our understanding of plant-viroid interactions and support for future mechanistic studies directed at delineating the functional role of candidate factors involved in viroid elimination.
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Affiliation(s)
- Ankita Shrestha
- Biology Centre, Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (A.S.); (J.M.); (V.S.N.); (P.A.); (T.K.)
| | - Ajay Kumar Mishra
- Biology Centre, Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (A.S.); (J.M.); (V.S.N.); (P.A.); (T.K.)
| | - Jaroslav Matoušek
- Biology Centre, Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (A.S.); (J.M.); (V.S.N.); (P.A.); (T.K.)
| | - Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6-Lysolaje, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (D.P.); (Z.Z.)
| | - Vishnu Sukumari Nath
- Biology Centre, Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (A.S.); (J.M.); (V.S.N.); (P.A.); (T.K.)
| | - Praveen Awasthi
- Biology Centre, Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (A.S.); (J.M.); (V.S.N.); (P.A.); (T.K.)
| | - Tomáš Kocábek
- Biology Centre, Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (A.S.); (J.M.); (V.S.N.); (P.A.); (T.K.)
| | - Jernej Jakse
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia;
| | - Lenka Záveská Drábková
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6-Lysolaje, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (D.P.); (Z.Z.)
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6-Lysolaje, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, D-40204 Düsseldorf, Germany;
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23
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Khitun A, Slavoff SA. Proteomic Detection and Validation of Translated Small Open Reading Frames. ACTA ACUST UNITED AC 2020; 11:e77. [PMID: 31750990 DOI: 10.1002/cpch.77] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small open reading frames (smORFs) encode previously unannotated polypeptides or short proteins that regulate translation in cis (eukaryotes) and/or are independently functional (prokaryotes and eukaryotes). Ongoing efforts for complete annotation and functional characterization of smORF-encoded proteins have yielded novel regulators and therapeutic targets. However, because they are excluded from protein databases, initiate at non-AUG start codons, and produce few unique tryptic peptides, unannotated small proteins cannot be detected with standard proteomic methods. Here,, we outline a procedure for mass spectrometry-based detection of translated smORFs in cultured human cells from protein extraction, digestion, and LC-MS/MS, to database preparation and data analysis. Following proteomic detection, translation from a unique smORF may be validated via siRNA-based silencing or overexpression and epitope tagging. This is necessary to unambiguously assign a peptide to a smORF within a specific transcript isoform or genomic locus. Provided that sufficient starting material is available, this workflow can be applied to any cell type/organism and adjusted to study specific (patho)physiological contexts including, but not limited to, development, stress, and disease. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Protein extraction, size selection, and trypsin digestion Alternate Protocol 1: In-solution C8 column size selection Support Protocol 1: Chloroform/methanol precipitation Support Protocol 2: Reduction, alkylation, and in-solution protease digestion Support Protocol 3: Peptide de-salting Basic Protocol 2: Two-dimensional LC-MS/MS with ERLIC fractionation Basic Protocol 3: Transcriptomic database construction Alternate Protocol 2: Transcriptomics database generation with gffread Basic Protocol 4: Non-annotated peptide identification from LC-MS/MS data Basic Protocol 5: Validation using isotopically labeled synthetic peptide standards and siRNA Basic Protocol 6: Transcript validation using transient overexpression.
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Affiliation(s)
- Alexandra Khitun
- Department of Chemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
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24
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Valdés A, Castro-Puyana M, García-Pastor C, Lucio-Cazaña FJ, Marina ML. Time-series proteomic study of the response of HK-2 cells to hyperglycemic, hypoxic diabetic-like milieu. PLoS One 2020; 15:e0235118. [PMID: 32579601 PMCID: PMC7313754 DOI: 10.1371/journal.pone.0235118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/09/2020] [Indexed: 12/13/2022] Open
Abstract
During diabetes, renal proximal tubular cells (PTC) are exposed to a combination of high glucose and hypoxic conditions, which plays a relevant role in the development of diabetic kidney disease (DKD). In this work, a time-series proteomic study was performed to analyse the effect of a diabetic-like microenvironment induced changes on HK-2 cells, a human cell line derived from normal proximal tubular epithelial cells. Cells simultaneously exposed to high glucose (25 mM) and hypoxia (1% O2) were compared to cells in control conditions for up to 48 h. Diabetic conditions increased the percentage of death cells after 24 and 48 h, but no differences in the protein/cell ratio were found. The relative protein quantification using dimethyl-labeling and UHPLC-MS/MS analysis allowed the identification of 317, 296 and 259 proteins at 5, 24 and 48 h, respectively. The combination of statistical and time expression profile analyses indicated an increased expression of proteins involved in glycolysis, and a decrease of cytoskeletal-related proteins. The exposure of HK-2 cells to high glucose and hypoxia reproduces some of the effects of diabetes on PTC and, with the limitations inherent to in vitro studies, propose new mechanisms and targets to be considered in the management of DKD.
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Affiliation(s)
- Alberto Valdés
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Alcalá de Henares, Madrid, España
| | - María Castro-Puyana
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Alcalá de Henares, Madrid, España
- Instituto de Investigación Química Andrés M del Rio, IQAR, Universidad de Alcalá, Alcalá de Henares, Madrid, España
| | - Coral García-Pastor
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá de Henares, Madrid, España
| | | | - María Luisa Marina
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Alcalá de Henares, Madrid, España
- Instituto de Investigación Química Andrés M del Rio, IQAR, Universidad de Alcalá, Alcalá de Henares, Madrid, España
- * E-mail:
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25
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Ondrej M, Rehulka P, Rehulkova H, Kupcik R, Tichy A. Fractionation of Enriched Phosphopeptides Using pH/Acetonitrile-Gradient-Reversed-Phase Microcolumn Separation in Combination with LC-MS/MS Analysis. Int J Mol Sci 2020; 21:ijms21113971. [PMID: 32492839 PMCID: PMC7312998 DOI: 10.3390/ijms21113971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
Mass spectrometry (MS) is a powerful and sensitive method often used for the identification of phosphoproteins. However, in phosphoproteomics, there is an identified need to compensate for the low abundance, insufficient ionization, and suppression effects of non-phosphorylated peptides. These may hamper the subsequent liquid chromatography–mass spectrometry/mass spectrometry (LC–MS/MS) analysis, resulting in incomplete phosphoproteome characterization, even when using high-resolution instruments. To overcome these drawbacks, we present here an effective microgradient chromatographic technique that yields specific fractions of enriched phosphopeptides compatible with LC–MS/MS analysis. The purpose of our study was to increase the number of identified phosphopeptides, and thus, the coverage of the sample phosphoproteome using the reproducible and straightforward fractionation method. This protocol includes a phosphopeptide enrichment step followed by the optimized microgradient fractionation of enriched phosphopeptides and final LC–MS/MS analysis of the obtained fractions. The simple fractionation system consists of a gas-tight microsyringe delivering the optimized gradient mobile phase to reversed-phase microcolumn. Our data indicate that combining the phosphopeptide enrichment with the microgradient separation is a promising technique for in-depth phosphoproteomic analysis due to moderate input material requirements and more than 3-fold enhanced protein identification.
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Affiliation(s)
- Martin Ondrej
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic; (M.O.); (H.R.)
| | - Pavel Rehulka
- Department of Molecular Biology and Pathology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic;
| | - Helena Rehulkova
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic; (M.O.); (H.R.)
| | - Rudolf Kupcik
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, 532 10 Pardubice, Czech Republic;
| | - Ales Tichy
- Department of Radiobiology, Faculty of Military Health Sciences, University of Defense in Brno, 500 01 Hradec Kralove, Czech Republic; (M.O.); (H.R.)
- Correspondence: ; Tel.: +420-973-253-216
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26
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Matoušek J, Steinbachová L, Drábková LZ, Kocábek T, Potěšil D, Mishra AK, Honys D, Steger G. Elimination of Viroids from Tobacco Pollen Involves a Decrease in Propagation Rate and an Increase of the Degradation Processes. Int J Mol Sci 2020; 21:E3029. [PMID: 32344786 PMCID: PMC7216239 DOI: 10.3390/ijms21083029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
Some viroids-single-stranded, non-coding, circular RNA parasites of plants-are not transmissible through pollen to seeds and to next generation. We analyzed the cause for the elimination of apple fruit crinkle viroid (AFCVd) and citrus bark cracking viroid (CBCVd) from male gametophyte cells of Nicotiana tabacum by RNA deep sequencing and molecular methods using infected and transformed tobacco pollen tissues at different developmental stages. AFCVd was not transferable from pollen to seeds in reciprocal pollinations, due to a complete viroid eradication during the last steps of pollen development and fertilization. In pollen, the viroid replication pathway proceeds with detectable replication intermediates, but is dramatically depressed in comparison to leaves. Specific and unspecific viroid degradation with some preference for (-) chains occurred in pollen, as detected by analysis of viroid-derived small RNAs, by quantification of viroid levels and by detection of viroid degradation products forming "comets" on Northern blots. The decrease of viroid levels during pollen development correlated with mRNA accumulation of several RNA-degrading factors, such as AGO5 nuclease, DICER-like and TUDOR S-like nuclease. In addition, the functional status of pollen, as a tissue with high ribosome content, could play a role during suppression of AFCVd replication involving transcription factors IIIA and ribosomal protein L5.
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Affiliation(s)
- Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (T.K.); (A.K.M.)
| | - Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Lenka Záveská Drábková
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Tomáš Kocábek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (T.K.); (A.K.M.)
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic;
| | - Ajay Kumar Mishra
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (T.K.); (A.K.M.)
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, D-40204 Düsseldorf, Germany
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27
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Klatt S, Roberts A, Lothian A, Masters CL, Cappai R, Fowler C, Roberts BR. Optimizing red blood cell protein extraction for biomarker quantitation with mass spectrometry. Anal Bioanal Chem 2020; 412:1879-1892. [PMID: 32030493 DOI: 10.1007/s00216-020-02439-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/11/2020] [Accepted: 01/17/2020] [Indexed: 10/25/2022]
Abstract
Red blood cells (RBC) are the most common cell type found in blood. They might serve as reservoir for biomarker research as they are anuclear and lack the ability to synthesize proteins. Not many biomarker assays, however, have been conducted on RBC because of their large dynamic range of proteins, high abundance of lipids, and hemoglobin interferences. Here, we developed a semiquantitative mass spectrometry-based assay that targeted 144 proteins and compared the efficiency of urea, sodium deoxycholate, acetonitrile, and HemoVoid™ in their extraction of the RBC proteome. Our results indicate that protein extraction with HemoVoid™ led to hemoglobin reduction and increased detection of low abundance proteins. Although hemoglobin interference after deoxycholate and urea extraction was high, there were adequate amounts of low abundance proteins for quantitation. Extraction with acetonitrile led to an overall decrease in protein abundances probably as a result of precipitation. Overall, the best compromise in sensitivity and sample processing time was achieved with the urea-trypsin digestion protocol. This provided the basis for large-scale evaluations of protein targets as potential blood-based biomarkers. As a proof of concept, we applied this assay to determine that alpha-synuclein, a prominent marker in Parkinson's disease, has an average concentration of approximately 40 μg mL-1 in RBC. This is important to know as the concentration of alpha-synuclein in plasma, typically in the picogram per milliliter range, might be partially derived from lysed RBC. Utilization of this assay will prove useful for future biomarker studies and provide a more complete analytical toolbox for the measurement of blood-derived proteins. Graphical abstract.
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Affiliation(s)
- Stephan Klatt
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia.,Cooperative Research Centre for Mental Health, Parkville, Victoria, 3052, Australia
| | - Anne Roberts
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia.,Cooperative Research Centre for Mental Health, Parkville, Victoria, 3052, Australia
| | - Amber Lothian
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia.,Cooperative Research Centre for Mental Health, Parkville, Victoria, 3052, Australia
| | - Colin L Masters
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia.,Cooperative Research Centre for Mental Health, Parkville, Victoria, 3052, Australia
| | - Roberto Cappai
- Department of Pharmacology and Therapeutics, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Christopher Fowler
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia.,Cooperative Research Centre for Mental Health, Parkville, Victoria, 3052, Australia
| | - Blaine R Roberts
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia. .,Cooperative Research Centre for Mental Health, Parkville, Victoria, 3052, Australia. .,Department of Biochemistry, Department of Neurology, School of Medicine, Emory University, Atlanta, GA, 30322, USA.
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28
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Roberts JT, Patel KR, Barb AW. Site-specific N-glycan Analysis of Antibody-binding Fc γ Receptors from Primary Human Monocytes. Mol Cell Proteomics 2020; 19:362-374. [PMID: 31888963 PMCID: PMC7000114 DOI: 10.1074/mcp.ra119.001733] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/10/2019] [Indexed: 12/29/2022] Open
Abstract
FcγRIIIa (CD16a) and FcγRIIa (CD32a) on monocytes are essential for proper effector functions including antibody dependent cellular cytotoxicity (ADCC) and phagocytosis (ADCP). Indeed, therapeutic monoclonal antibodies (mAbs) that bind FcγRs with greater affinity exhibit greater efficacy. Furthermore, post-translational modification impacts antibody binding affinity, most notably the composition of the asparagine(N)-linked glycan at N162 of CD16a. CD16a is widely recognized as the key receptor for the monocyte response, however the post-translational modifications of CD16a from endogenous monocytes are not described. Here we isolated monocytes from individual donors and characterized the composition of CD16a and CD32a N-glycans from all modified sites. The composition of CD16a N-glycans varied by glycosylation site and donor. CD16a displayed primarily complex-type biantennary N-glycans at N162, however some individuals expressed CD16a V158 with ∼20% hybrid and oligomannose types which increased affinity for IgG1 Fc according to surface plasmon resonance binding analyses. The CD16a N45-glycans contain markedly less processing than other sites with >75% hybrid and oligomannose forms. N38 and N74 of CD16a both contain highly processed complex-type N-glycans with N-acetyllactosamine repeats and complex-type biantennary N-glycans dominate at N169. The composition of CD16a N-glycans isolated from monocytes included a higher proportion of oligomannose-type N-glycans at N45 and less sialylation plus greater branch fucosylation than we observed in a recent analysis of NK cell CD16a. The additional analysis of CD32a from monocytes revealed different features than observed for CD16a including the presence of a predominantly biantennary complex-type N-glycans with two sialic acids at both sites (N64 and N145).
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Affiliation(s)
- Jacob T Roberts
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames Iowa 50011
| | - Kashyap R Patel
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames Iowa 50011
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames Iowa 50011
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
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29
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Sousa Neto IV, Carvalho MM, Marqueti RDC, Almeida JA, Oliveira KDS, Barin FR, Petriz B, Araújo HSS, Franco OL, Durigan JLQ. Proteomic changes in skeletal muscle of aged rats in response to resistance training. Cell Biochem Funct 2020; 38:500-509. [DOI: 10.1002/cbf.3497] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/09/2019] [Accepted: 12/23/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Ivo Vieira Sousa Neto
- Programa de Pós‐Graduação em Ciências e Tecnologias em SaúdeUniversidade de Brasília – UnB Brasília DF Brazil
| | - Marcia Mendes Carvalho
- Programa de Pós‐graduação em Educação FísicaUniversidade de Brasília – UnB Brasília DF Brazil
| | - Rita de Cassia Marqueti
- Programa de Pós‐Graduação em Ciências e Tecnologias em SaúdeUniversidade de Brasília – UnB Brasília DF Brazil
- Programa de Pós‐graduação em Ciências da ReabilitaçãoUniversidade de Brasília – UnB Brasília DF Brazil
| | - Jeeser Alves Almeida
- Pesquisa em Exercício e Nutrição na Saúde e Rendimento Esportivo – PENSARE, Programa de Pós‐Graduação em Ciências do MovimentoUniversidade Federal de Mato Grosso do Sul – UFMS Campo Grande MS Brazil
| | - Kléber de S. Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de Brasília – UCB Brasília DF Brazil
| | - Fabrício R. Barin
- Programa de Pós‐Graduação em Ciências e Tecnologias em SaúdeUniversidade de Brasília – UnB Brasília DF Brazil
| | - Bernardo Petriz
- Centro de Análises Proteômicas e Bioquímicas, Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de Brasília – UCB Brasília DF Brazil
| | | | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de Brasília – UCB Brasília DF Brazil
- Programa de Pós‐Graduação em BiotecnologiaUniversidade Católica Dom Bosco – UCDB Campo Grande MS Brazil
| | - João Luiz Quaglioti Durigan
- Programa de Pós‐Graduação em Ciências e Tecnologias em SaúdeUniversidade de Brasília – UnB Brasília DF Brazil
- Programa de Pós‐graduação em Educação FísicaUniversidade de Brasília – UnB Brasília DF Brazil
- Programa de Pós‐graduação em Ciências da ReabilitaçãoUniversidade de Brasília – UnB Brasília DF Brazil
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30
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Patel KR, Nott JD, Barb AW. Primary Human Natural Killer Cells Retain Proinflammatory IgG1 at the Cell Surface and Express CD16a Glycoforms with Donor-dependent Variability. Mol Cell Proteomics 2019; 18:2178-2190. [PMID: 31467031 PMCID: PMC6823852 DOI: 10.1074/mcp.ra119.001607] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/02/2019] [Indexed: 11/06/2022] Open
Abstract
Post-translational modification confers diverse functional properties to immune system proteins. The composition of serum proteins such as immunoglobulin G (IgG) strongly associates with disease including forms lacking a fucose modification of the crystallizable fragment (Fc) asparagine(N)-linked glycan that show increased effector function, however, virtually nothing is known about the composition of cell surface receptors or their bound ligands in situ because of low abundance in the circulating blood. We isolated primary NK cells from apheresis filters following plasma or platelet donation to characterize the compositional variability of Fc γ receptor IIIa/CD16a and its bound ligand, IgG1. CD16a N162-glycans showed the largest differences between donors; one donor displayed only oligomannose-type N-glycans at N162 that correlate with high affinity IgG1 Fc binding whereas the other donors displayed a high degree of compositional variability at this site. Hybrid-type N-glycans with intermediate processing dominated at N45 and highly modified, complex-type N-glycans decorated N38 and N74 from all donors. Analysis of the IgG1 ligand bound to NK cell CD16a revealed a sharp decrease in antibody fucosylation (43.2 ± 11.0%) versus serum from the same donors (89.7 ± 3.9%). Thus, NK cells express CD16a with unique modification patterns and preferentially bind IgG1 without the Fc fucose modification at the cell surface.
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Affiliation(s)
- Kashyap R Patel
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames IA 50011
| | - Joel D Nott
- Office of Biotechnology, Protein Facility, Iowa State University, Ames IA 50011
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames IA 50011; Department of Biochemistry and Molecular Biology, University of Georgia, Athens 30602; Complex Carbohydrate Research Center, University of Georgia, Athens 30602.
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Evasion of autophagy mediated by Rickettsia surface protein OmpB is critical for virulence. Nat Microbiol 2019; 4:2538-2551. [PMID: 31611642 PMCID: PMC6988571 DOI: 10.1038/s41564-019-0583-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 09/10/2019] [Indexed: 01/05/2023]
Abstract
Rickettsia are obligate intracellular bacteria that evade antimicrobial autophagy in the host cell cytosol by unknown mechanisms. Other cytosolic pathogens block different steps of autophagy targeting, including the initial step of polyubiquitin-coat formation. One mechanism of evasion is to mobilize actin to the bacterial surface. Here, we show that actin mobilization is insufficient to block autophagy recognition of the pathogen Rickettsia parkeri. Instead, R. parkeri employs outer membrane protein B (OmpB) to block ubiquitylation of the bacterial surface proteins, including OmpA, and subsequent recognition by autophagy receptors. OmpB is also required for the formation of a capsule-like layer. Although OmpB is dispensable for bacterial growth in endothelial cells, it is essential for R. parkeri to block autophagy in macrophages and to colonize mice because of its ability to promote autophagy evasion in immune cells. Our results indicate that OmpB acts as a protective shield to obstruct autophagy recognition, thereby revealing a distinctive bacterial mechanism to evade antimicrobial autophagy.
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32
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Channaveerappa D, Ngounou Wetie AG, Darie CC. Bottlenecks in Proteomics: An Update. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:753-769. [PMID: 31347083 DOI: 10.1007/978-3-030-15950-4_45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Mass spectrometry (MS) is the core for advanced methods in proteomic experiments. When effectively used, proteomics may provide extensive information about proteins and their post-translational modifications, as well as their interaction partners. However, there are also many problems that one can encounter during a proteomic experiment, including, but not limited to sample preparation, sample fractionation, sample analysis, data analysis & interpretation and biological significance. Here we discuss some of the problems that researchers should be aware of when performing a proteomic experiment.
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Affiliation(s)
- Devika Channaveerappa
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Armand G Ngounou Wetie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA.
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Carlson ML, Stacey RG, Young JW, Wason IS, Zhao Z, Rattray DG, Scott N, Kerr CH, Babu M, Foster LJ, Duong Van Hoa F. Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries. eLife 2019; 8:46615. [PMID: 31364989 PMCID: PMC6697469 DOI: 10.7554/elife.46615] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Protein-correlation-profiling (PCP), in combination with quantitative proteomics, has emerged as a high-throughput method for the rapid identification of dynamic protein complexes in native conditions. While PCP has been successfully applied to soluble proteomes, characterization of the membrane interactome has lagged, partly due to the necessary use of detergents to maintain protein solubility. Here, we apply the peptidisc, a ‘one-size fits all’ membrane mimetic, for the capture of the Escherichia coli cell envelope proteome and its high-resolution fractionation in the absence of detergent. Analysis of the SILAC-labeled peptidisc library via PCP allows generation of over 4900 possible binary interactions out of >700,000 random associations. Using well-characterized membrane protein systems such as the SecY translocon, the Bam complex and the MetNI transporter, we demonstrate that our dataset is a useful resource for identifying transient and surprisingly novel protein interactions. For example, we discover a trans-periplasmic supercomplex comprising subunits of the Bam and Sec machineries, including membrane-bound chaperones YfgM and PpiD. We identify RcsF and OmpA as bone fide interactors of BamA, and we show that MetQ association with the ABC transporter MetNI depends on its N-terminal lipid anchor. We also discover NlpA as a novel interactor of MetNI complex. Most of these interactions are largely undetected by standard detergent-based purification. Together, the peptidisc workflow applied to the proteomic field is emerging as a promising novel approach to characterize membrane protein interactions under native expression conditions and without genetic manipulation.
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Affiliation(s)
- Michael Luke Carlson
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - R Greg Stacey
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - John William Young
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Irvinder Singh Wason
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Zhiyu Zhao
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - David G Rattray
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Nichollas Scott
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Craig H Kerr
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Mohan Babu
- Department of Biochemistry, Faculty of Science, University of Regina, Regina, Canada
| | - Leonard J Foster
- Michael Smith Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Franck Duong Van Hoa
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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Buitinga M, Callebaut A, Marques Câmara Sodré F, Crèvecoeur I, Blahnik-Fagan G, Yang ML, Bugliani M, Arribas-Layton D, Marré M, Cook DP, Waelkens E, Mallone R, Piganelli JD, Marchetti P, Mamula MJ, Derua R, James EA, Mathieu C, Overbergh L. Inflammation-Induced Citrullinated Glucose-Regulated Protein 78 Elicits Immune Responses in Human Type 1 Diabetes. Diabetes 2018; 67:2337-2348. [PMID: 30348823 PMCID: PMC6973547 DOI: 10.2337/db18-0295] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/31/2018] [Indexed: 12/16/2022]
Abstract
The β-cell has become recognized as a central player in the pathogenesis of type 1 diabetes with the generation of neoantigens as potential triggers for breaking immune tolerance. We report that posttranslationally modified glucose-regulated protein 78 (GRP78) is a novel autoantigen in human type 1 diabetes. When human islets were exposed to inflammatory stress induced by interleukin-1β, tumor necrosis factor-α, and interferon-γ, arginine residue R510 within GRP78 was converted into citrulline, as evidenced by liquid chromatography-tandem mass spectrometry. This conversion, known as citrullination, led to the generation of neoepitopes, which effectively could be presented by HLA-DRB1*04:01 molecules. With the use of HLA-DRB1*04:01 tetramers and ELISA techniques, we demonstrate enhanced antigenicity of citrullinated GRP78 with significantly increased CD4+ T-cell responses and autoantibody titers in patients with type 1 diabetes compared with healthy control subjects. Of note, patients with type 1 diabetes had a predominantly higher percentage of central memory cells and a lower percentage of effector memory cells directed against citrullinated GRP78 compared with the native epitope. These results strongly suggest that citrullination of β-cell proteins, exemplified here by the citrullination of GRP78, contributes to loss of self-tolerance toward β-cells in human type 1 diabetes, indicating that β-cells actively participate in their own demise.
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Affiliation(s)
- Mijke Buitinga
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Aïsha Callebaut
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | | | - Inne Crèvecoeur
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | | | | | | | | | - Meghan Marré
- Division of Pediatric Surgery, University of Pittsburgh, Pittsburgh, PA
| | - Dana P Cook
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Etienne Waelkens
- Laboratory of Protein Phosphorylation and Proteomics, KU Leuven, Leuven, Belgium
- SyBioMa, KU Leuven, Leuven, Belgium
| | - Roberto Mallone
- INSERM, U1016, CNRS, UMR8104, Paris Descartes University, Sorbonne Paris Cité, Cochin Institute, Paris, France
| | - Jon D Piganelli
- Division of Pediatric Surgery, University of Pittsburgh, Pittsburgh, PA
| | | | | | - Rita Derua
- Laboratory of Protein Phosphorylation and Proteomics, KU Leuven, Leuven, Belgium
- SyBioMa, KU Leuven, Leuven, Belgium
| | | | - Chantal Mathieu
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Lut Overbergh
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
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35
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Palomo L, Mleczko JE, Azkargorta M, Conde-Vancells J, González E, Elortza F, Royo F, Falcon-Perez JM. Abundance of Cytochromes in Hepatic Extracellular Vesicles Is Altered by Drugs Related With Drug-Induced Liver Injury. Hepatol Commun 2018; 2:1064-1079. [PMID: 30202821 PMCID: PMC6128234 DOI: 10.1002/hep4.1210] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/01/2018] [Indexed: 12/14/2022] Open
Abstract
Drug‐induced liver injury (DILI) is a serious worldwide health problem that accounts for more than 50% of acute liver failure. There is a great interest in clinical diagnosis and pharmaceutical industry to elucidate underlying molecular mechanisms and find noninvasive biomarkers for this pathology. Cell‐secreted extracellular vesicles (EVs) have provided a new biological source to identify low disease invasive markers. Despite the intense research developed on these vesicles, there is currently a gap on their patho‐physiological effects. Here, we study EVs secreted by primary rat hepatocytes challenged with galactatosamine (GalN), acetaminophen, or diclofenac as DILI in vitromodels. Proteomics analysis of these EVs revealed an increase in enzymes already associated with liver damage, such as catecholamine‐methyl transferase and arginase 1. An increase in translation‐related proteins and a decrease in regulators of apoptosis were also observed. In addition, we show the presence of enzymatic activity of P450 cytochrome 2d1 in EVs. The activity specifically is decreased in EVs secreted by hepatocytes after acetaminophen treatment and increased in EVs derived from GalN‐treated hepatocytes. By using in vivo preclinical models, we demonstrate the presence of this cytochrome activity in circulation under normal conditions and an increased activity after GalN‐induced injury. Conclusion: Hepatocyte‐secreted EVs carry active xenobiotic‐metabolizing enzymes that might be relevant in extracellular metabolism of drugs and be associated with DILI. (Hepatology Communications 2018;0:00‐00)
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Affiliation(s)
- Laura Palomo
- Exosomes Laboratory, CIC bioGUNE, CIBERehd Bizkaia Spain
| | | | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed Bizkaia Spain
| | | | | | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed Bizkaia Spain
| | - Félix Royo
- Exosomes Laboratory, CIC bioGUNE, CIBERehd Bizkaia Spain
| | - Juan M Falcon-Perez
- Exosomes Laboratory, CIC bioGUNE, CIBERehd Bizkaia Spain.,IKERBASQUE, Basque Foundation for Science Bilbao Spain
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Šalovská B, Janečková H, Fabrik I, Karlíková R, Čecháková L, Ondrej M, Link M, Friedecký D, Tichý A. Radio-sensitizing effects of VE-821 and beyond: Distinct phosphoproteomic and metabolomic changes after ATR inhibition in irradiated MOLT-4 cells. PLoS One 2018; 13:e0199349. [PMID: 30001349 PMCID: PMC6042708 DOI: 10.1371/journal.pone.0199349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/06/2018] [Indexed: 12/13/2022] Open
Abstract
Current anti-cancer strategy takes advantage of tumour specific abnormalities in DNA damage response to radio- or chemo-therapy. Inhibition of the ATR/Chk1 pathway has been shown to be synthetically lethal in cells with high levels of oncogene-induced replication stress and in p53- or ATM- deficient cells. In the presented study, we aimed to elucidate molecular mechanisms underlying radiosensitization of T-lymphocyte leukemic MOLT-4 cells by VE-821, a higly potent and specific inhibitor of ATR. We combined multiple approaches: cell biology techniques to reveal the inhibitor-induced phenotypes, and quantitative proteomics, phosphoproteomics, and metabolomics to comprehensively describe drug-induced changes in irradiated cells. VE-821 radiosensitized MOLT-4 cells, and furthermore 10 μM VE-821 significantly affected proliferation of sham-irradiated MOLT-4 cells. We detected 623 differentially regulated phosphorylation sites. We revealed changes not only in DDR-related pathways and kinases, but also in pathways and kinases involved in maintaining cellular metabolism. Notably, we found downregulation of mTOR, the main regulator of cellular metabolism, which was most likely caused by an off-target effect of the inhibitor, and we propose that mTOR inhibition could be one of the factors contributing to the phenotype observed after treating MOLT-4 cells with 10 μM VE-821. In the metabolomic analysis, 206 intermediary metabolites were detected. The data indicated that VE-821 potentiated metabolic disruption induced by irradiation and affected the response to irradiation-induced oxidative stress. Upon irradiation, recovery of damaged deoxynucleotides might be affected by VE-821, hampering DNA repair by their deficiency. Taken together, this is the first study describing a complex scenario of cellular events that might be ATR-dependent or triggered by ATR inhibition in irradiated MOLT-4 cells. Data are available via ProteomeXchange with identifier PXD008925.
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Affiliation(s)
- Barbora Šalovská
- Department of Radiobiology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, Hradec Králové, Czech Republic
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Janečková
- Laboratory for Inherited Metabolic Disorders, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
- Department of Clinical Biochemistry, University Hospital Olomouc, Olomouc, Czech Republic
| | - Ivo Fabrik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, Hradec Králové, Czech Republic
- Biomedical Research Center, University Hospital, Hradec Králové, Czech Republic
| | - Radana Karlíková
- Department of Clinical Biochemistry, University Hospital Olomouc, Olomouc, Czech Republic
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Lucie Čecháková
- Department of Radiobiology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, Hradec Králové, Czech Republic
| | - Martin Ondrej
- Department of Radiobiology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, Hradec Králové, Czech Republic
| | - Marek Link
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, Hradec Králové, Czech Republic
| | - David Friedecký
- Laboratory for Inherited Metabolic Disorders, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
- Department of Clinical Biochemistry, University Hospital Olomouc, Olomouc, Czech Republic
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Aleš Tichý
- Department of Radiobiology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, Hradec Králové, Czech Republic
- Biomedical Research Center, University Hospital, Hradec Králové, Czech Republic
- * E-mail:
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Abstract
Peptidomics is an emerging field focused in the analysis of endogenous peptides. Naturally occurring peptides are often endogenously produced protein fragments. Cleavage of precursor proteins by proteases generates peptides that may gain specialized functions not ascribed to their precursors, and which could reflect the state of a cell under certain physiological conditions or pathological processes.Since peptides are found in complex matrices (e.g., serum, tear, urine, cerebrospinal fluid), they need to be isolated from the matrix and concentrated before they can be analyzed on mass spectrometry. This chapter describes methods for sample preparation prior to mass spectrometry analysis. In addition, different peptide fragmentation techniques are described which are complementary when analyzing naturally occurring peptides by liquid chromatography coupled online to tandem mass spectrometry.
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38
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Oikawa K, Inomata T, Hirao Y, Yamamoto T, Baslam M, Kaneko K, Mitsui T. Proteomic Analysis of Rice Golgi Membranes Isolated by Floating Through Discontinuous Sucrose Density Gradient. Methods Mol Biol 2018; 1696:91-105. [PMID: 29086398 DOI: 10.1007/978-1-4939-7411-5_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The Golgi apparatus is an endomembrane system organelle and has roles in glycosylation, sorting, and secretion of proteins in the secretory pathway. It has a central function in living organism and is also essential for plant growth. Proteomic approaches to identify the Golgi membrane proteins have been performed in cell suspension cultures and many Golgi membrane-associated proteins were found, whereas it has well established in rice seedling yet. In this chapter, our recent improving published methods for isolated rice Golgi membranes by floating through a discontinuous sucrose density gradient are provided in detail with proteomic analyses.
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Affiliation(s)
- Kazusato Oikawa
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
| | - Takuya Inomata
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181, Japan
| | - Yoshitoshi Hirao
- Biofluid Biomarker Center, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181, Japan
| | - Tadashi Yamamoto
- Biofluid Biomarker Center, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181, Japan
| | - Marouane Baslam
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181, Japan
| | - Kentaro Kaneko
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181, Japan
| | - Toshiaki Mitsui
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan.
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata, 950-2181, Japan.
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Fabrik I, Link M, Putzova D, Plzakova L, Lubovska Z, Philimonenko V, Pavkova I, Rehulka P, Krocova Z, Hozak P, Santic M, Stulik J. The Early Dendritic Cell Signaling Induced by Virulent Francisella tularensis Strain Occurs in Phases and Involves the Activation of Extracellular Signal-Regulated Kinases (ERKs) and p38 In the Later Stage. Mol Cell Proteomics 2017; 17:81-94. [PMID: 29046388 DOI: 10.1074/mcp.ra117.000160] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/22/2017] [Indexed: 12/18/2022] Open
Abstract
Dendritic cells (DCs) infected by Francisella tularensis are poorly activated and do not undergo classical maturation process. Although reasons of such unresponsiveness are not fully understood, their impact on the priming of immunity is well appreciated. Previous attempts to explain the behavior of Francisella-infected DCs were hypothesis-driven and focused on events at later stages of infection. Here, we took an alternative unbiased approach by applying methods of global phosphoproteomics to analyze the dynamics of cell signaling in primary DCs during the first hour of infection by Francisella tularensis Presented results show that the early response of DCs to Francisella occurs in phases and that ERK and p38 signaling modules induced at the later stage are differentially regulated by virulent and attenuated ΔdsbA strain. These findings imply that the temporal orchestration of host proinflammatory pathways represents the integral part of Francisella life-cycle inside hijacked DCs.
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Affiliation(s)
- Ivo Fabrik
- From the ‡Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, 500 01 Hradec Kralove, Czech Republic
| | - Marek Link
- From the ‡Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, 500 01 Hradec Kralove, Czech Republic
| | - Daniela Putzova
- From the ‡Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, 500 01 Hradec Kralove, Czech Republic
| | - Lenka Plzakova
- From the ‡Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, 500 01 Hradec Kralove, Czech Republic
| | - Zuzana Lubovska
- §Institute of Molecular Genetics ASCR v.v.i., Microscopy Centre, Electron Microscopy Core Facility, 142 20 Prague 4, Czech Republic
| | - Vlada Philimonenko
- §Institute of Molecular Genetics ASCR v.v.i., Microscopy Centre, Electron Microscopy Core Facility, 142 20 Prague 4, Czech Republic.,¶Institute of Molecular Genetics ASCR v.v.i., Department of Biology of the Cell Nucleus, 142 20 Prague 4, Czech Republic
| | - Ivona Pavkova
- From the ‡Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, 500 01 Hradec Kralove, Czech Republic
| | - Pavel Rehulka
- From the ‡Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, 500 01 Hradec Kralove, Czech Republic
| | - Zuzana Krocova
- From the ‡Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, 500 01 Hradec Kralove, Czech Republic
| | - Pavel Hozak
- §Institute of Molecular Genetics ASCR v.v.i., Microscopy Centre, Electron Microscopy Core Facility, 142 20 Prague 4, Czech Republic.,¶Institute of Molecular Genetics ASCR v.v.i., Department of Biology of the Cell Nucleus, 142 20 Prague 4, Czech Republic
| | - Marina Santic
- ‖Department of Microbiology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Jiri Stulik
- From the ‡Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, 500 01 Hradec Kralove, Czech Republic;
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Valdés A, García-Cañas V, Pérez-Sánchez A, Barrajón-Catalán E, Ruiz-Torres V, Artemenko KA, Micol V, Bergquist J, Cifuentes A. Shotgun proteomic analysis to study the decrease of xenograft tumor growth after rosemary extract treatment. J Chromatogr A 2017; 1499:90-100. [PMID: 28389096 DOI: 10.1016/j.chroma.2017.03.072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 03/23/2017] [Accepted: 03/25/2017] [Indexed: 12/18/2022]
Abstract
The antiproliferative activity of Rosemary (Rosmarinus officinalis) has been widely studied in different in vitro and in vivo models, which demonstrate that rosemary extracts inhibit the cellular proliferation due to its ability to interact with a wide spectrum of molecular targets. However, a comprehensive proteomics study in vivo has not been carried out yet. In the present work, the effects of rosemary extract on xenograft tumor growth has been studied and, for the first time, a shotgun proteomic analysis based on nano-LC-MS/MS together with stable isotope dimethyl labeling (DML) has been applied to investigate the global protein changes in vivo. Our results show that the daily administration of a polyphenol-enriched rosemary extract reduces the progression of colorectal cancer in vivo with the subsequent deregulation of 74 proteins. The bioinformatic analysis of these proteins indicates that the rosemary extract mainly alters the RNA Post-Transcriptional Modification, the Protein Synthesis and the Amino Acid Metabolism functions and suggests the inactivation of the oncogene MYC. These results demonstrate the high utility of the proposed analytical methodology to determine, simultaneously, the expression levels of a large number of protein biomarkers and to generate new hypothesis about the molecular mechanisms of this extract in vivo.
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Affiliation(s)
- Alberto Valdés
- Laboratory of Foodomics, Institute of Food Science Research (CIAL, CSIC), Nicolas Cabrera 9, 28049, Madrid, Spain
| | - Virginia García-Cañas
- Molecular Nutrition and Metabolism, Institute of Food Science Research (CIAL, CSIC), Nicolas Cabrera 9, 28049 Madrid, Spain
| | - Almudena Pérez-Sánchez
- Institute of Molecular and Cellular Biology, Miguel Hernández University, Avda. Universidad s/n, Elche 03202, Spain
| | - Enrique Barrajón-Catalán
- Institute of Molecular and Cellular Biology, Miguel Hernández University, Avda. Universidad s/n, Elche 03202, Spain
| | - Verónica Ruiz-Torres
- Institute of Molecular and Cellular Biology, Miguel Hernández University, Avda. Universidad s/n, Elche 03202, Spain
| | - Konstantin A Artemenko
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Husargatan 3, 75124 Uppsala, Sweden
| | - Vicente Micol
- Institute of Molecular and Cellular Biology, Miguel Hernández University, Avda. Universidad s/n, Elche 03202, Spain; CIBER, Fisiopatología de la Obesidad y la Nutrición, CIBERobn, Instituto de Salud Carlos III (CB12/03/30038), Spain
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Husargatan 3, 75124 Uppsala, Sweden
| | - Alejandro Cifuentes
- Laboratory of Foodomics, Institute of Food Science Research (CIAL, CSIC), Nicolas Cabrera 9, 28049, Madrid, Spain.
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41
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Valdés A, García-Cañas V, Artemenko KA, Simó C, Bergquist J, Cifuentes A. Nano-liquid Chromatography-orbitrap MS-based Quantitative Proteomics Reveals Differences Between the Mechanisms of Action of Carnosic Acid and Carnosol in Colon Cancer Cells. Mol Cell Proteomics 2016; 16:8-22. [PMID: 27834734 DOI: 10.1074/mcp.m116.061481] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/24/2016] [Indexed: 11/06/2022] Open
Abstract
Carnosic acid (CA) and carnosol (CS) are two structurally related diterpenes present in rosemary herb (Rosmarinus officinalis). Although several studies have demonstrated that both diterpenes can scavenge free radicals and interfere in cellular processes such as cell proliferation, they may not necessarily exert the same effects at the molecular level. In this work, a shotgun proteomics study based on stable isotope dimethyl labeling (DML) and nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) has been performed to identify the relative changes in proteins and to gain some light on the specific molecular targets and mechanisms of action of CA and CS in HT-29 colon cancer cells. Protein profiles revealed that CA and CS induce different Nrf2-mediated response. Furthermore, examination of our data revealed that each diterpene affects protein homeostasis by different mechanisms. CA treatment induces the expression of proteins involved in the unfolded protein response in a concentration dependent manner reflecting ER stress, whereas CS directly inhibits chymotrypsin-like activity of the 20S proteasome. In conclusion, the unbiased proteomics-wide method applied in the present study has demonstrated to be a powerful tool to reveal differences on the mechanisms of action of two related bioactive compounds in the same biological model.
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Affiliation(s)
- Alberto Valdés
- From the ‡Laboratory of Foodomics, Institute of Food Science Research (CIAL, CSIC), Calle Nicolás Cabrera 9, 28049 Madrid, Spain
| | - Virginia García-Cañas
- From the ‡Laboratory of Foodomics, Institute of Food Science Research (CIAL, CSIC), Calle Nicolás Cabrera 9, 28049 Madrid, Spain;
| | - Konstantin A Artemenko
- §Analytical Chemistry, Department of Chemistry-BMC and SciLifeLab, Uppsala University, Husargatan 3, 75124 Uppsala, Sweden
| | - Carolina Simó
- From the ‡Laboratory of Foodomics, Institute of Food Science Research (CIAL, CSIC), Calle Nicolás Cabrera 9, 28049 Madrid, Spain
| | - Jonas Bergquist
- §Analytical Chemistry, Department of Chemistry-BMC and SciLifeLab, Uppsala University, Husargatan 3, 75124 Uppsala, Sweden
| | - Alejandro Cifuentes
- From the ‡Laboratory of Foodomics, Institute of Food Science Research (CIAL, CSIC), Calle Nicolás Cabrera 9, 28049 Madrid, Spain
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42
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Phetsang W, Pelingon R, Butler MS, KC S, Pitt ME, Kaeslin G, Cooper MA, Blaskovich MAT. Fluorescent Trimethoprim Conjugate Probes To Assess Drug Accumulation in Wild Type and Mutant Escherichia coli. ACS Infect Dis 2016; 2:688-701. [PMID: 27737551 PMCID: PMC5067704 DOI: 10.1021/acsinfecdis.6b00080] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Reduced
susceptibility to antimicrobials in Gram-negative bacteria may result
from multiple resistance mechanisms, including increased efflux pump
activity or reduced porin protein expression. Up-regulation of the
efflux pump system is closely associated with multidrug resistance
(MDR). To help investigate the role of efflux pumps on compound accumulation,
a fluorescence-based assay was developed using fluorescent derivatives
of trimethoprim (TMP), a broad-spectrum synthetic antibiotic that
inhibits an intracellular target, dihydrofolate reductase (DHFR).
Novel fluorescent TMP probes inhibited eDHFR activity
with comparable potency to TMP, but did not kill or inhibit growth
of wild type Escherichia coli. However,
bactericidal activity was observed against an efflux pump deficient E. coli mutant strain (ΔtolC). A simple and quick fluorescence assay was developed to measure
cellular accumulation of the TMP probe using either fluorescence spectroscopy
or flow cytometry, with validation by LC-MS/MS. This fluorescence
assay may provide a simple method to assess efflux pump activity with
standard laboratory equipment.
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Affiliation(s)
- Wanida Phetsang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ruby Pelingon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark S. Butler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sanjaya KC
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Miranda E. Pitt
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Geraldine Kaeslin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark A. T. Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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43
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Valdés A, Artemenko KA, Bergquist J, García-Cañas V, Cifuentes A. Comprehensive Proteomic Study of the Antiproliferative Activity of a Polyphenol-Enriched Rosemary Extract on Colon Cancer Cells Using Nanoliquid Chromatography–Orbitrap MS/MS. J Proteome Res 2016; 15:1971-85. [DOI: 10.1021/acs.jproteome.6b00154] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alberto Valdés
- Laboratory
of Foodomics, Institute of Food Science Research (CIAL, CSIC), Calle Nicolás Cabrera 9, 28049 Madrid, Spain
| | - Konstantin A. Artemenko
- Analytical
Chemistry, Department of Chemistry-BMC and SciLifeLab, Uppsala University, Husargatan 3, 75124 Uppsala, Sweden
| | - Jonas Bergquist
- Analytical
Chemistry, Department of Chemistry-BMC and SciLifeLab, Uppsala University, Husargatan 3, 75124 Uppsala, Sweden
| | - Virginia García-Cañas
- Laboratory
of Foodomics, Institute of Food Science Research (CIAL, CSIC), Calle Nicolás Cabrera 9, 28049 Madrid, Spain
| | - Alejandro Cifuentes
- Laboratory
of Foodomics, Institute of Food Science Research (CIAL, CSIC), Calle Nicolás Cabrera 9, 28049 Madrid, Spain
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44
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Sample Preparation for Mass Spectrometry-Based Proteomics; from Proteomes to Peptides. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:43-62. [DOI: 10.1007/978-3-319-41448-5_3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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45
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Hill RC, Oman TJ, Shan G, Schafer B, Eble J, Chen C. Development and Validation of a Multiplexed Protein Quantitation Assay for the Determination of Three Recombinant Proteins in Soybean Tissues by Liquid Chromatography with Tandem Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:7450-61. [PMID: 26237374 DOI: 10.1021/acs.jafc.5b03083] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Currently, traditional immunochemistry technologies such as enzyme-linked immunosorbent assays (ELISA) are the predominant analytical tool used to measure levels of recombinant proteins expressed in genetically engineered (GE) plants. Recent advances in agricultural biotechnology have created a need to develop methods capable of selectively detecting and quantifying multiple proteins in complex matrices because of increasing numbers of transgenic proteins being coexpressed or "stacked" to achieve tolerance to multiple herbicides or to provide multiple modes of action for insect control. A multiplexing analytical method utilizing liquid chromatography with tandem mass spectrometry (LC-MS/MS) has been developed and validated to quantify three herbicide-tolerant proteins in soybean tissues: aryloxyalkanoate dioxygenase (AAD-12), 5-enol-pyruvylshikimate-3-phosphate synthase (2mEPSPS), and phosphinothricin acetyltransferase (PAT). Results from the validation showed high recovery and precision over multiple analysts and laboratories. Results from this method were comparable to those obtained with ELISA with respect to protein quantitation, and the described method was demonstrated to be suitable for multiplex quantitation of transgenic proteins in GE crops.
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Affiliation(s)
- Ryan C Hill
- Dow AgroSciences, LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Trent J Oman
- Dow AgroSciences, LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Guomin Shan
- Dow AgroSciences, LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Barry Schafer
- Dow AgroSciences, LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Julie Eble
- Critical Path Services, LLC , 3070 McCann Farm Drive, Garnet Valley, Pennsylvania 19060, United States
| | - Cynthia Chen
- Critical Path Services, LLC , 3070 McCann Farm Drive, Garnet Valley, Pennsylvania 19060, United States
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46
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Feist P, Hummon AB. Proteomic challenges: sample preparation techniques for microgram-quantity protein analysis from biological samples. Int J Mol Sci 2015; 16:3537-63. [PMID: 25664860 PMCID: PMC4346912 DOI: 10.3390/ijms16023537] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/29/2015] [Indexed: 12/22/2022] Open
Abstract
Proteins regulate many cellular functions and analyzing the presence and abundance of proteins in biological samples are central focuses in proteomics. The discovery and validation of biomarkers, pathways, and drug targets for various diseases can be accomplished using mass spectrometry-based proteomics. However, with mass-limited samples like tumor biopsies, it can be challenging to obtain sufficient amounts of proteins to generate high-quality mass spectrometric data. Techniques developed for macroscale quantities recover sufficient amounts of protein from milligram quantities of starting material, but sample losses become crippling with these techniques when only microgram amounts of material are available. To combat this challenge, proteomicists have developed micro-scale techniques that are compatible with decreased sample size (100 μg or lower) and still enable excellent proteome coverage. Extraction, contaminant removal, protein quantitation, and sample handling techniques for the microgram protein range are reviewed here, with an emphasis on liquid chromatography and bottom-up mass spectrometry-compatible techniques. Also, a range of biological specimens, including mammalian tissues and model cell culture systems, are discussed.
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Affiliation(s)
- Peter Feist
- Department of Chemistry and Biochemistry, Integrated Biomedical Sciences Program, and the Harper Cancer Research Institute, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Integrated Biomedical Sciences Program, and the Harper Cancer Research Institute, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA.
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47
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Krahmer J, Hindle MM, Martin SF, Le Bihan T, Millar AJ. Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana. Methods Enzymol 2014; 551:405-31. [PMID: 25662467 PMCID: PMC4427183 DOI: 10.1016/bs.mie.2014.10.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Systems biological approaches to study the Arabidopsis thaliana circadian clock have mainly focused on transcriptomics while little is known about the proteome, and even less about posttranslational modifications. Evidence has emerged that posttranslational protein modifications, in particular phosphorylation, play an important role for the clock and its output. Phosphoproteomics is the method of choice for a large-scale approach to gain more knowledge about rhythmic protein phosphorylation. Recent plant phosphoproteomics publications have identified several thousand phosphopeptides. However, the methods used in these studies are very labor-intensive and therefore not suitable to apply to a well-replicated circadian time series. To address this issue, we present and compare different strategies for sample preparation for phosphoproteomics that are compatible with large numbers of samples. Methods are compared regarding number of identifications, variability of quantitation, and functional categorization. We focus on the type of detergent used for protein extraction as well as methods for its removal. We also test a simple two-fraction separation of the protein extract.
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Affiliation(s)
- Johanna Krahmer
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Matthew M Hindle
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah F Martin
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Thierry Le Bihan
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
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48
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The removal of Triton X-100 by dialysis is feasible! Anal Bioanal Chem 2014; 407:1107-18. [DOI: 10.1007/s00216-014-8333-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 11/06/2014] [Accepted: 11/07/2014] [Indexed: 10/24/2022]
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49
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Radiosensitization of human leukemic HL-60 cells by ATR kinase inhibitor (VE-821): phosphoproteomic analysis. Int J Mol Sci 2014; 15:12007-26. [PMID: 25003641 PMCID: PMC4139827 DOI: 10.3390/ijms150712007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 04/18/2014] [Accepted: 04/28/2014] [Indexed: 01/18/2023] Open
Abstract
DNA damaging agents such as ionizing radiation or chemotherapy are frequently used in oncology. DNA damage response (DDR)-triggered by radiation-induced double strand breaks-is orchestrated mainly by three Phosphatidylinositol 3-kinase-related kinases (PIKKs): Ataxia teleangiectasia mutated (ATM), DNA-dependent protein kinase (DNA-PK) and ATM and Rad3-related kinase (ATR). Their activation promotes cell-cycle arrest and facilitates DNA damage repair, resulting in radioresistance. Recently developed specific ATR inhibitor, VE-821 (3-amino-6-(4-(methylsulfonyl)phenyl)-N-phenylpyrazine-2-carboxamide), has been reported to have a significant radio- and chemo-sensitizing effect delimited to cancer cells (largely p53-deficient) without affecting normal cells. In this study, we employed SILAC-based quantitative phosphoproteomics to describe the mechanism of the radiosensitizing effect of VE-821 in human promyelocytic leukemic cells HL-60 (p53-negative). Hydrophilic interaction liquid chromatography (HILIC)-prefractionation with TiO2-enrichment and nano-liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis revealed 9834 phosphorylation sites. Proteins with differentially up-/down-regulated phosphorylation were mostly localized in the nucleus and were involved in cellular processes such as DDR, all phases of the cell cycle, and cell division. Moreover, sequence motif analysis revealed significant changes in the activities of kinases involved in these processes. Taken together, our data indicates that ATR kinase has multiple roles in response to DNA damage throughout the cell cycle and that its inhibitor VE-821 is a potent radiosensitizing agent for p53-negative HL-60 cells.
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50
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Roy SJ, Glazkova I, Fréchette L, Iorio-Morin C, Binda C, Pétrin D, Trieu P, Robitaille M, Angers S, Hébert TE, Parent JL. Novel, gel-free proteomics approach identifies RNF5 and JAMP as modulators of GPCR stability. Mol Endocrinol 2013; 27:1245-66. [PMID: 23798571 DOI: 10.1210/me.2013-1091] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The maturation and folding of G protein-coupled receptors are governed by mechanisms that remain poorly understood. In an effort to characterize these biological events, we optimized a novel, gel-free proteomic approach to identify partners of the β2-adrenergic receptor (β2AR). In addition to a number of known interacting proteins such as heterotrimeric G protein subunits, this allowed us to identify proteins involved in endoplasmic reticulum (ER) QC of the receptor. Among β2AR-associated proteins is Ring finger protein 5 (RNF5), an E3 ubiquitin ligase anchored to the outer membrane of the ER. Coimmunoprecipitation assays confirmed, in a cellular context, the interaction between RNF5 and the β2AR as well as the prostaglandin D2 receptor (DP). Confocal microscopy revealed that DP colocalized with RNF5 at the ER. Coexpression of RNF5 with either receptor increased levels of their expression, whereas small interfering RNA-mediated knockdown of endogenous RNF5 promoted the opposite. RNF5 did not modulate the ubiquitination state of β2AR or DP. Instead, RNF5 ubiquitinated JNK-associated membrane protein (JAMP), a protein that recruits the proteasome to the ER membrane and that is negatively regulated by RNF5-mediated ubiquitination. JAMP coimmunoprecipitated with both β2AR and DP and decreased total receptor protein levels through proteasomal degradation. Expression of DP, a receptor largely retained in the ER, promoted proteasome recruitment by JAMP. Degradation of both receptors via JAMP was increased when RNF5 was depleted. Our data suggest that RNF5 regulates the turnover of specific G protein-coupled receptors by ubiquitinating JAMP and preventing proteasome recruitment.
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Affiliation(s)
- Sébastien J Roy
- Service de Rhumatologie Département de Médecine, Université de Sherbrooke, the Institut de Pharmacologie de Sherbrooke, and the Centre de Recherche Clinique Etienne-Lebel, Sherbrooke, Québec J1H 5N4, Canada
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