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Wang X, Li H, Wu C, Yang J, Wang J, Yang T. Metabolism-triggered sensor array aided by machine learning for rapid identification of pathogens. Biosens Bioelectron 2024; 255:116264. [PMID: 38588629 DOI: 10.1016/j.bios.2024.116264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/28/2024] [Accepted: 03/31/2024] [Indexed: 04/10/2024]
Abstract
Chemical-nose strategy has achieved certain success in the discrimination and identification of pathogens. However, this strategy usually relies on non-specific interactions, which are prone to be significantly disturbed by the change of environment thus limiting its practical usefulness. Herein, we present a novel chemical-nose sensing approach leveraging the difference in the dynamic metabolic variation during peptidoglycan metabolism among different species for rapid pathogen discrimination. Pathogens were first tethered with clickable handles through metabolic labeling at two different acidities (pH = 5 and 7) for 20 and 60 min, respectively, followed by click reaction with fluorescence up-conversion nanoparticles to generate a four-dimensional signal output. This discriminative multi-dimensional signal allowed eight types of model bacteria to be successfully classified within the training set into strains, genera, and Gram phenotypes. As the difference in signals of the four sensing channels reflects the difference in the amount/activity of enzymes involved in metabolic labeling, this strategy has good anti-interference capability, which enables precise pathogen identification within 2 h with 100% accuracy in spiked urinary samples and allows classification of unknown species out of the training set into the right phenotype. The robustness of this approach holds significant promise for its widespread application in pathogen identification and surveillance.
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Affiliation(s)
- Xin Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Huida Li
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Chengxin Wu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jianyu Yang
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Jianhua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Ting Yang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China.
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2
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Suazo KF, Mishra V, Maity S, Auger SA, Justyna K, Petre AM, Ottoboni L, Ongaro J, Corti SP, Lotti F, Przedborski S, Distefano MD. Improved synthesis and application of an alkyne-functionalized isoprenoid analogue to study the prenylomes of motor neurons, astrocytes and their stem cell progenitors. Bioorg Chem 2024; 147:107365. [PMID: 38636436 DOI: 10.1016/j.bioorg.2024.107365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024]
Abstract
Protein prenylation is one example of a broad class of post-translational modifications where proteins are covalently linked to various hydrophobic moieties. To globally identify and monitor levels of all prenylated proteins in a cell simultaneously, our laboratory and others have developed chemical proteomic approaches that rely on the metabolic incorporation of isoprenoid analogues bearing bio-orthogonal functionality followed by enrichment and subsequent quantitative proteomic analysis. Here, several improvements in the synthesis of the alkyne-containing isoprenoid analogue C15AlkOPP are reported to improve synthetic efficiency. Next, metabolic labeling with C15AlkOPP was optimized to obtain useful levels of metabolic incorporation of the probe in several types of primary cells. Those conditions were then used to study the prenylomes of motor neurons (ES-MNs), astrocytes (ES-As), and their embryonic stem cell progenitors (ESCs), which allowed for the identification of 54 prenylated proteins from ESCs, 50 from ES-MNs, and 84 from ES-As, representing all types of prenylation. Bioinformatic analysis revealed specific enriched pathways, including nervous system development, chemokine signaling, Rho GTPase signaling, and adhesion. Hierarchical clustering showed that most enriched pathways in all three cell types are related to GTPase activity and vesicular transport. In contrast, STRING analysis showed significant interactions in two populations that appear to be cell type dependent. The data provided herein demonstrates that robust incorporation of C15AlkOPP can be obtained in ES-MNs and related primary cells purified via magnetic-activated cell sorting allowing the identification and quantification of numerous prenylated proteins. These results suggest that metabolic labeling with C15AlkOPP should be an effective approach for investigating the role of prenylated proteins in primary cells in both normal cells and disease pathologies, including ALS.
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Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Vartika Mishra
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032, USA; Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032, USA.
| | - Sanjay Maity
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Shelby A Auger
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Katarzyna Justyna
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Alexandru M Petre
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
| | - Jessica Ongaro
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania P Corti
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - Francesco Lotti
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032, USA; Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032, USA.
| | - Serge Przedborski
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032, USA; Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032, USA; Department of Neuroscience, Pathology, and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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3
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Jurėnas D. Metabolic Labeling: Snapshot of the Effect of Toxins on the Key Cellular Processes. Methods Mol Biol 2024; 2715:539-545. [PMID: 37930550 DOI: 10.1007/978-1-0716-3445-5_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Competing bacteria secrete vast variety of toxic effectors via secretion systems. Phospholipase, peptidoglycan-hydrolase, or pore forming toxins often manifest in the bursting of the prey cell. Other toxins reach cytoplasm of the prey where they affect cell division machinery, metabolism, nucleic acid integrity, or protein synthesis. Inhibition of cell division or DNA integrity, which summons SOS response, will often lead to bacterial cell filamentation readily observable under the microscope. However, other toxic activities will not manifest in interpretable phenotypic changes that would readily suggest their mechanism of toxicity. Activity measurements of the three fundamental cellular processes-replication, transcription and translation can pave the way for further understanding of the toxin's activity. Method commonly known as metabolic labeling makes use of radioactive precursors for DNA, RNA and protein synthesis. This method provides highly sensitive snapshot of the activity of key cellular processes.
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Affiliation(s)
- Dukas Jurėnas
- Laboratoire de Génétique et Physiologie Bactérienne, Département de Biologie Moléculaire, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium.
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4
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Guay KP, Ke H, Gierasch LM, Gershenson A, Hebert DN. Monitoring the Secretion and Activity of Alpha-1 Antitrypsin in Various Mammalian Cell Types. Methods Mol Biol 2024; 2750:143-163. [PMID: 38108975 PMCID: PMC10918612 DOI: 10.1007/978-1-0716-3605-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Overexpression of recombinant protein in mammalian cells is widely used for producing biologics, as protein maturation and post-translational modifications are similar to human cells. Some therapeutics, such as mRNA vaccines, target nonnative cells that may contain inefficient secretory machinery. For example, gene replacement therapies for alpha-1 antitrypsin (AAT), a glycoprotein normally produced in hepatocytes, are often targeted to muscle cells due to ease of delivery. In this chapter, we define methods for expressing AAT in representative cell types such as Huh-7; hepatocytes; Chinese hamster ovarian cells (CHO), a common host to produce biologics; and C2C12, a muscle progenitor cell line. Methods for metabolically labeling AAT to monitor secretion in these cell lines are described along with the use of proteostasis activators to increase the amount of AAT secreted in both C2C12 myoblasts and differentiated myotubes. Assays to assess the activity and glycan composition of overexpressed AAT are also presented. The usage of the proteostasis activator SAHA provided a 40% improvement in expression of active AAT in muscle-like cells and may be an advantageous adjuvant for recombinant production of proteins delivered by mRNA vaccines.
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Affiliation(s)
- Kevin P Guay
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Haiping Ke
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Daniel N Hebert
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA.
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA.
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5
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Tavakoli S, Evans A, Oommen OP, Creemers L, Nandi JB, Hilborn J, Varghese OP. Unveiling extracellular matrix assembly: Insights and approaches through bioorthogonal chemistry. Mater Today Bio 2023; 22:100768. [PMID: 37600348 PMCID: PMC10432810 DOI: 10.1016/j.mtbio.2023.100768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/22/2023] Open
Abstract
Visualizing cells, tissues, and their components specifically without interference with cellular functions, such as biochemical reactions, and cellular viability remains important for biomedical researchers worldwide. For an improved understanding of disease progression, tissue formation during development, and tissue regeneration, labeling extracellular matrix (ECM) components secreted by cells persists is required. Bioorthogonal chemistry approaches offer solutions to visualizing and labeling ECM constituents without interfering with other chemical or biological events. Although biorthogonal chemistry has been studied extensively for several applications, this review summarizes the recent advancements in using biorthogonal chemistry specifically for metabolic labeling and visualization of ECM proteins and glycosaminoglycans that are secreted by cells and living tissues. Challenges, limitations, and future directions surrounding biorthogonal chemistry involved in the labeling of ECM components are discussed. Finally, potential solutions for improvements to biorthogonal chemical approaches are suggested. This would provide theoretical guidance for labeling and visualization of de novo proteins and polysaccharides present in ECM that are cell-secreted for example during tissue remodeling or in vitro differentiation of stem cells.
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Affiliation(s)
- Shima Tavakoli
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
| | - Austin Evans
- Bioengineering and Nanomedicine Group, Faculty of Medicine and Health Technologies, Tampere University, 33720, Tampere, Finland
| | - Oommen P. Oommen
- Bioengineering and Nanomedicine Group, Faculty of Medicine and Health Technologies, Tampere University, 33720, Tampere, Finland
| | - Laura Creemers
- Department of Orthopedics, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Jharna Barman Nandi
- Department of Chemistry, Sarojini Naidu College for Women, 30 Jessore Road, Kolkata, 700028, India
| | - Jöns Hilborn
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
| | - Oommen P. Varghese
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
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6
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Kirschner F, Arnold-Schild D, Leps C, Łącki MK, Klein M, Chen Y, Ludt A, Marini F, Kücük C, Stein L, Distler U, Sielaff M, Michna T, Riegel K, Rajalingam K, Bopp T, Tenzer S, Schild H. Modulation of cellular transcriptome and proteome composition by azidohomoalanine-implications on click chemistry-based secretome analysis. J Mol Med (Berl) 2023; 101:855-867. [PMID: 37231147 PMCID: PMC10300158 DOI: 10.1007/s00109-023-02333-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/25/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
The analysis of the secretome provides important information on proteins defining intercellular communication and the recruitment and behavior of cells in specific tissues. Especially in the context of tumors, secretome data can support decisions for diagnosis and therapy. The mass spectrometry-based analysis of cell-conditioned media is widely used for the unbiased characterization of cancer secretomes in vitro. Metabolic labeling using azide-containing amino acid analogs in combination with click chemistry facilitates this type of analysis in the presence of serum, preventing serum starvation-induced effects. The modified amino acid analogs, however, are less efficiently incorporated into newly synthesized proteins and may perturb protein folding. Combining transcriptome and proteome analysis, we elucidate in detail the effects of metabolic labeling with the methionine analog azidohomoalanine (AHA) on gene and protein expression. Our data reveal that 15-39% of the proteins detected in the secretome displayed changes in transcript and protein expression induced by AHA labeling. Gene Ontology (GO) analyses indicate that metabolic labeling using AHA leads to induction of cellular stress and apoptosis-related pathways and provide first insights on how this affects the composition of the secretome on a global scale. KEY MESSAGES: Azide-containing amino acid analogs affect gene expression profiles. Azide-containing amino acid analogs influence cellular proteome. Azidohomoalanine labeling induces cellular stress and apoptotic pathways. Secretome consists of proteins with dysregulated expression profiles.
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Affiliation(s)
- Friederike Kirschner
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Danielle Arnold-Schild
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Christian Leps
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Mateusz Krzysztof Łącki
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Matthias Klein
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Yannic Chen
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany
| | - Annekathrin Ludt
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Can Kücük
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany
| | - Lara Stein
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Ute Distler
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Malte Sielaff
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Thomas Michna
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Kristina Riegel
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tobias Bopp
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- University Cancer Center Mainz, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany.
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany.
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany.
- Helmholtz Institute Translational Oncology, Obere Zahlbacher Straße 63, 55131, Mainz, Germany.
- Research Center for Immunotherapy (FZI), Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
- University Cancer Center Mainz, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
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7
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Xu Y, Lin H. Use of alkyne-tagged myristic acid to detect N-terminal myristoylation. Methods Enzymol 2023; 684:191-208. [PMID: 37230589 DOI: 10.1016/bs.mie.2023.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Protein N-terminal myristoylation is a lipidic modification typically occurring to the α-amino group of N-terminal glycine residues of proteins. It is catalyzed by the N-myristoyltransferase (NMT) enzyme family. Many studies in the past three decades have highlighted the importance of N-terminal glycine myristoylation as it affects protein localization, protein-protein interaction, and protein stability, thereby regulating multiple biological processes, including immune cell signaling, cancer progression, and infections. This book chapter will present protocols for using alkyne-tagged myristic acid to detect the N-myristoylation of targeted proteins in cell lines and compare global N-myristoylation levels. We then described a protocol of SILAC proteomics that compare the levels of N-myristoylation on a proteomic scale. These assays allow for the identification of potential NMT substrates and the development of novel NMT inhibitors.
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Affiliation(s)
- Yilai Xu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States; Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States.
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8
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Smolka JA, Lewis SC. In Situ Analysis of Mitochondrial DNA Synthesis Using Metabolic Labeling Coupled to Fluorescence Microscopy. Methods Mol Biol 2023; 2615:99-106. [PMID: 36807787 DOI: 10.1007/978-1-0716-2922-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Metabolic labeling with the nucleoside analog 5-ethynyl-2'-deoxyuridine (EdU) enables the selective labeling of DNA synthesis in live cells. Newly synthesized EdU-containing DNA can be covalently modified after extraction or in fixed cells using copper-catalyzed azide-alkyne cycloaddition "click chemistry" reactions, enabling bioconjugation to various substrates including fluorophores for imaging studies. While often used to study nuclear DNA replication, EdU labeling can also be leveraged to detect the synthesis of organellar DNA in the cytoplasm of Eukaryotic cells. In this chapter, we outline methods for the application of EdU labeling to the study of mitochondrial genome synthesis in fixed cultured human cells, using fluorescent labeling and superresolution light microscopy.
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Affiliation(s)
- John A Smolka
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Samantha C Lewis
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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9
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Kim J, Seo S, Kim TY. Metabolic deuterium oxide (D 2O) labeling in quantitative omics studies: A tutorial review. Anal Chim Acta 2023; 1242:340722. [PMID: 36657897 DOI: 10.1016/j.aca.2022.340722] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/25/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Mass spectrometry (MS) is an invaluable tool for sensitive detection and characterization of individual biomolecules in omics studies. MS combined with stable isotope labeling enables the accurate and precise determination of quantitative changes occurring in biological samples. Metabolic isotope labeling, wherein isotopes are introduced into biomolecules through biosynthetic metabolism, is one of the main labeling strategies. Among the precursors employed in metabolic isotope labeling, deuterium oxide (D2O) is cost-effective and easy to implement in any biological systems. This tutorial review aims to explain the basic principle of D2O labeling and its applications in omics research. D2O labeling incorporates D into stable C-H bonds in various biomolecules, including nucleotides, proteins, lipids, and carbohydrates. Typically, D2O labeling is performed at low enrichment of 1%-10% D2O, which causes subtle changes in the isotopic distribution of a biomolecule, instead of the complete separation between labeled and unlabeled samples in a mass spectrum. D2O labeling has been employed in various omics studies to determine the metabolic flux, turnover rate, and relative quantification. Moreover, the advantages and challenges of D2O labeling and its future prospects in quantitative omics are discussed. The economy, versatility, and convenience of D2O labeling will be beneficial for the long-term omics studies for higher organisms.
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Affiliation(s)
- Jonghyun Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Seungwoo Seo
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Tae-Young Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea.
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10
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Zaia J. The 2022 Nobel Prize in Chemistry for the development of click chemistry and bioorthogonal chemistry. Anal Bioanal Chem 2023; 415:527-532. [PMID: 36602567 PMCID: PMC10848669 DOI: 10.1007/s00216-022-04483-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023]
Abstract
The 2022 Nobel Prize in Chemistry recognized the development of biorthogonal chemical ligation reactions known as click chemistry in biomedicine. This concept has catalyzed significant progress in sensing and diagnosis, chemical biology, materials chemistry, and drug discovery and delivery. In proteomics, the ability to incorporate a click tag into proteins has propelled development of powerful new methods for selective enrichment of protein complexes that inform understanding of protein networks. It also has had a strong influence on the ability to enrich for protein post-translational modifications. This feature article summarizes the impacts of biorthogonal click chemistry on proteomics.
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Affiliation(s)
- Joseph Zaia
- Dept. of Biochemistry, Boston University, 670 Albany St. Rm. 509, Boston, MA, 02118, USA.
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11
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Wang J, Cao W, Zhang W, Dou B, Zeng X, Su S, Cao H, Ding X, Ma J, Li X. Ac 34FGlcNAz is an effective metabolic chemical reporter for O-GlcNAcylated proteins with decreased S-glyco-modification. Bioorg Chem 2023; 131:106139. [PMID: 36610251 DOI: 10.1016/j.bioorg.2022.106139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 02/02/2023]
Abstract
O-GlcNAcylation is a ubiquitous post-translational modification governing vital biological processes in cancer, diabetes and neurodegeneration. Metabolic chemical reporters (MCRs) containing bio-orthogonal groups such as azido or alkyne, are widely used for labeling of interested proteins. However, most MCRs developed for O-GlcNAc modification are not specific and always lead to unexpected side reactions termed S-glyco-modification. Here, we attempt to develop a new MCR of Ac34FGlcNAz that replacing the 4-OH of Ac4GlcNAz with fluorine, which is supposed to abolish the epimerization of GALE and enhance the selectivity. The discoveries demonstrate that Ac34FGlcNAz is a powerful MCR for O-GlcNAcylation with high efficiency and the process of this labeling is conducted by the two enzymes of OGT and OGA. Most importantly, Ac34FGlcNAz is predominantly incorporated intracellular proteins in the form of O-linkage and leads to negligible S-glyco-modification, indicating it is a selective MCR for O-GlcNAcylation. Therefore, we reason that Ac34FGlcNAz developed here is a well characterized MCR of O-GlcNAcylation, which provides more choice for label and enrichment of O-GlcNAc associated proteins.
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Affiliation(s)
- Jiajia Wang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng 475000, China
| | - Wei Cao
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng 475000, China
| | - Wei Zhang
- School of Pharmacy, Institute for Innovative Drug Design and Evaluation, Henan University, Kaifeng 475000, China
| | - Biao Dou
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng 475000, China
| | - Xueke Zeng
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng 475000, China
| | - Shihao Su
- School of Pharmacy, Institute for Innovative Drug Design and Evaluation, Henan University, Kaifeng 475000, China
| | - Hongtai Cao
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng 475000, China
| | - Xin Ding
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng 475000, China
| | - Jing Ma
- School of Pharmacy, Institute for Innovative Drug Design and Evaluation, Henan University, Kaifeng 475000, China.
| | - Xia Li
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng 475000, China.
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12
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Galiano MR, Hallak ME. Assaying the Posttranslational Arginylation of Proteins in Cultured Cells. Methods Mol Biol 2023; 2620:51-61. [PMID: 37010748 DOI: 10.1007/978-1-0716-2942-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
To evaluate the posttranslational arginylation of proteins in vivo, we describe a protocol for studying the 14C-Arg incorporation into proteins of cells in culture. The conditions determined for this particular modification contemplate both the biochemical requirements of the enzyme ATE1 and the adjustments that allowed the discrimination between posttranslational arginylation of proteins and de novo synthesis. These conditions are applicable for different cell lines or primary cultures, representing an optimal procedure for the identification and the validation of putative ATE1 substrates.
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Affiliation(s)
- Mauricio R Galiano
- Dpt. Quimica Biologica Ranwel Caputto, Facultad de Ciencias Quimicas, Universidad Nacional de Córdoba, CIQUIBIC-CONICET, Córdoba, Argentina
| | - Marta E Hallak
- Dpt. Quimica Biologica Ranwel Caputto, Facultad de Ciencias Quimicas, Universidad Nacional de Córdoba, CIQUIBIC-CONICET, Córdoba, Argentina.
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13
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Fang C, Zhang X, Lu H. Quantification of Protein Palmitoylation by Cysteine-SILAC. Methods Mol Biol 2023; 2603:59-69. [PMID: 36370270 DOI: 10.1007/978-1-0716-2863-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cysteine-SILAC enables the detection and quantification of protein S-palmitoylation, an important protein posttranslational modification. Here we describe the cell culture, protein extraction, selective enrichment, mass spectrometry, and data analysis for palmitoylated proteins from cell samples by this method.
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Affiliation(s)
- Caiyun Fang
- Department of Chemistry, Fudan University, Shanghai, China.
| | - Xiaoqin Zhang
- Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, China
| | - Haojie Lu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
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14
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Massignani E, Maniaci M, Bonaldi T. Heavy Methyl SILAC Metabolic Labeling of Human Cell Lines for High-Confidence Identification of R/K-Methylated Peptides by High-Resolution Mass Spectrometry. Methods Mol Biol 2023; 2603:173-186. [PMID: 36370279 DOI: 10.1007/978-1-0716-2863-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein methylation is a widespread post-translational modification (PTM) involved in several important biological processes including, but not limited to, RNA splicing, signal transduction, translation, and DNA repair. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is considered today the most versatile and accurate technique to profile PTMs with high precision and proteome-wide depth; however, the identification of protein methylations by MS is still prone to high false discovery rates. In this chapter, we describe the heavy methyl SILAC metabolic labeling strategy that allows high-confidence identification of in vivo methyl-peptides by MS-based proteomics. We provide a general protocol that covers the steps of heavy methyl labeling of cultured cells, protein sample preparation, LC-MS/MS analysis, and downstream computational analysis of the acquired MS data.
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Affiliation(s)
- Enrico Massignani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- European School of Molecular Medicine (SEMM), Milan, Italy
| | - Marianna Maniaci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- European School of Molecular Medicine (SEMM), Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
- Department of Oncology and Haemathology-Oncology, University of MIlan, Milano, Italy.
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15
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Paulsen M. Ensuring Quality Cell Input for Single Cell Sequencing Experiments by Viability and Singlet Enrichment Using Cell Sorting. Methods Mol Biol 2023; 2584:183-9. [PMID: 36495449 DOI: 10.1007/978-1-0716-2756-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
As with every sensitive analysis technology, the golden principle of "input quality rules output quality" also applies to single cell sequencing methods. Given the sensitivity of the current methods in single cell sequencing and the minuscule amounts of RNA present within a single cell, any extrinsic source of variability should be reduced by ensuring a homogenous input right at the start. Not every tissue is as readily handled as a single cell suspension like blood and most tissues will have to undergo digestions to free the cells from their spatial organization to undergo single cell transcriptomics workflows. This chapter provides working protocols for two simple, but very precise and powerful methods to ensure only the most viable cells are introduced into single cell assays.
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16
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Chen B, Guarino C, Azzi A, Erb H, Wu X. Regulation of Cell Polarity by Posttranslational Protein Palmitoylation. Methods Mol Biol 2022; 2438:107-21. [PMID: 35147938 DOI: 10.1007/978-1-0716-2035-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cell polarity is a common feature of many living cells, especially epithelial cells, and plays important roles in development, tissue homeostasis, and diseases. Therefore, the signaling pathways involved in establishing and maintaining cell polarity are tightly controlled. Protein S-palmitoylation has been recently recognized as an important posttranslational modification involved in cell polarity, via dynamic covalent attachment of fatty acyl groups to the cysteine residues of cell polarity proteins. Here, we describe the methods to study the function and regulation of S-palmitoylation of cell polarity proteins.
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17
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Paggi RA, Albaum SP, Poetsch A, Cerletti M. Proteome Turnover Analysis in Haloferax volcanii by a Heavy Isotope Multilabeling Approach. Methods Mol Biol 2022; 2522:267-286. [PMID: 36125756 DOI: 10.1007/978-1-0716-2445-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The cellular protein repertoire is highly dynamic and responsive to internal or external stimuli. Its changes are largely the consequence of the combination of protein synthesis and degradation, referred collectively as protein turnover. Different proteomics techniques have been developed to determine the whole proteome turnover of a cell, but very few have been applied to archaea. In this chapter we describe a heavy isotope multilabeling method that allowed the successful analysis of relative protein synthesis and degradation rates on the proteome scale of the halophilic archaeon Haloferax volcanii. This method combines 15N and 13C isotope metabolic labeling with high-resolution mass spectrometry and data analysis tools (QuPE web-based platform) and could be applied to different archaea.
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Affiliation(s)
- Roberto A Paggi
- Instituto de Investigaciones Biológicas, FCEyN, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - Stefan P Albaum
- Bioinformatics Resource Facility, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Ansgar Poetsch
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Queen Mary School, Medical College, Nanchang University, Nanchang, China.
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany.
| | - Micaela Cerletti
- Instituto de Investigaciones Biológicas, FCEyN, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina.
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18
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Nilsson I, Six DA. Metabolic Incorporation of Azido-Sugars into LPS to Enable Live-Cell Fluorescence Imaging. Methods Mol Biol 2022; 2548:267-278. [PMID: 36151503 DOI: 10.1007/978-1-0716-2581-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Metabolic labeling of lipopolysaccharides (LPS) with the exogenous azido analog of 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) or Kdo-N3 allows for both live-cell and molecular analysis of the outer membrane composition and biosynthesis in different Gram-negative bacteria. Here, we describe Kdo-N3 incorporation into bacterial cells, followed by click labeling with a fluorescent dye. The fluorescently labeled LPS can be analyzed from lysed cells by SDS-PAGE and from intact cells by microscopy and flow cytometry. These methods have been applied to the Gram-negative bacteria Escherichia coli and Klebsiella pneumoniae, which possess the sialic acid transporter NanT that is also capable of transporting exogenous Kdo and Kdo analogs into the cytoplasm for incorporation into nascent LPS.
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Affiliation(s)
- Inga Nilsson
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - David A Six
- hemotune AG, Schlieren, Switzerland.
- Venatorx Pharmaceuticals, Inc., Malvern, PA, USA.
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19
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Veraldi N, Dentand Quadri I, de Agostini A. Characterization of a spontaneous cell line from primary mouse fibroblasts as a model to study Sanfilippo syndrome. Int J Biochem Cell Biol 2021; 142:106119. [PMID: 34823007 DOI: 10.1016/j.biocel.2021.106119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/21/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022]
Abstract
To evaluate a new approach to Mucopolysaccharidosis type IIIA (MPS-IIIA), work was initiated on primary fibroblasts from a well-known mouse model in which sulfamidase deficiency correlates with the accumulation of heparan sulfate - the hallmark of this disease. Once the culture of fibroblasts was established, we observed continuous proliferation with a rapid growth rate, loss of contact inhibition and late passage stability, corresponding to a spontaneously immortalized cell line. The presence of the single point D31N mutation was verified and both rapid and abundant intracellular accumulation of low molecular weight HS was observed, confirming both genotype and phenotype. This cell line is a potential in vitro model system for future studies of MPS-IIIA prior to employing animal models.
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Affiliation(s)
- Noemi Veraldi
- Division of Clinical Pathology, Department of Diagnostics, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Isabelle Dentand Quadri
- Department of Pathology and Immunology, Faculty of Medicine, Geneva University, 1205 Geneva, Switzerland
| | - Ariane de Agostini
- Division of Clinical Pathology, Department of Diagnostics, Geneva University Hospitals, 1211 Geneva, Switzerland; Department of Pathology and Immunology, Faculty of Medicine, Geneva University, 1205 Geneva, Switzerland.
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20
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Echevarría C, Gutierrez C, Desvoyes B. Tools for Assessing Cell-Cycle Progression in Plants. Plant Cell Physiol 2021; 62:1231-1238. [PMID: 34021583 PMCID: PMC8579159 DOI: 10.1093/pcp/pcab066] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/27/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
Estimation of cell-cycle parameters is crucial for understanding the developmental programs established during the formation of an organism. A number of complementary approaches have been developed and adapted to plants to assess the cell-cycle status in different proliferative tissues. The most classical methods relying on metabolic labeling are still very much employed and give valuable information on cell-cycle progression in fixed tissues. However, the growing knowledge of plant cell-cycle regulators with defined expression pattern together with the development of fluorescent proteins technology enabled the generation of fusion proteins that function individually or in conjunction as cell-cycle reporters. Together with the improvement of imaging techniques, in vivo live imaging to monitor plant cell-cycle progression in normal growth conditions or in response to different stimuli has been possible. Here, we review these tools and their specific outputs for plant cell-cycle analysis.
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Affiliation(s)
- Clara Echevarría
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, Madrid 28049, Spain
| | - Crisanto Gutierrez
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, Madrid 28049, Spain
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21
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Gutierrez-Reyes CD, Jiang P, Atashi M, Bennett A, Yu A, Peng W, Zhong J, Mechref Y. Advances in mass spectrometry-based glycoproteomics: An update covering the period 2017-2021. Electrophoresis 2021; 43:370-387. [PMID: 34614238 DOI: 10.1002/elps.202100188] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/30/2021] [Accepted: 09/25/2021] [Indexed: 12/23/2022]
Abstract
Protein glycosylation is one of the most common posttranslational modifications, and plays an essential role in a wide range of biological processes such as immune response, intercellular signaling, inflammation, host-pathogen interaction, and protein stability. Glycoproteomics is a proteomics subfield dedicated to identifying and characterizing the glycans and glycoproteins in a given cell or tissue. Aberrant glycosylation has been associated with various diseases such as Alzheimer's disease, viral infections, inflammation, immune deficiencies, congenital disorders, and cancers. However, glycoproteomic analysis remains challenging because of the low abundance, site-specific heterogeneity, and poor ionization efficiency of glycopeptides during LC-MS analyses. Therefore, the development of sensitive and accurate approaches to efficiently characterize protein glycosylation is crucial. Methods such as metabolic labeling, enrichment, and derivatization of glycopeptides, coupled with different mass spectrometry techniques and bioinformatics tools, have been developed to achieve sophisticated levels of quantitative and qualitative analyses of glycoproteins. This review attempts to update the recent developments in the field of glycoproteomics reported between 2017 and 2021.
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Affiliation(s)
| | - Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Andrew Bennett
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Jieqiang Zhong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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22
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Ke X, Li C, Luo D, Wang T, Liu Y, Tan Z, Du M, He Z, Wang H, Zheng Z, Zhang Y. Metabolic labeling of enterovirus 71 with quantum dots for the study of virus receptor usage. J Nanobiotechnology 2021; 19:295. [PMID: 34583708 PMCID: PMC8477995 DOI: 10.1186/s12951-021-01046-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/16/2021] [Indexed: 11/10/2022] Open
Abstract
Fluorescent labeling and dynamic tracking is a powerful tool for exploring virus infection mechanisms. However, for small-sized viruses, virus tracking studies are usually hindered by a lack of appropriate labeling methods that do not dampen virus yield or infectivity. Here, we report a universal strategy for labeling viruses with chemical dyes and Quantum dots (QDs). Enterovirus 71 (EV71) was produced in a cell line that stably expresses a mutant methionyl-tRNA synthetase (MetRS), which can charge azidonorleucine (ANL) to the methionine sites of viral proteins during translation. Then, the ANL-containing virus was easily labeled with DBCO-AF647 and DBCO-QDs. The labeled virus shows sufficient yield and no obvious decrease in infectivity and can be used for imaging the virus entry process. Using the labeled EV71, different functions of scavenger receptor class B, member 2 (SCARB2), and heparan sulfate (HS) in EV71 infection were comparatively studied. The cell entry process of a strong HS-binding EV71 strain was investigated by real-time dynamic visualization of EV71-QDs in living cells. Taken together, our study described a universal biocompatible virus labeling method, visualized the dynamic viral entry process, and reported details of the receptor usage of EV71.
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Affiliation(s)
- Xianliang Ke
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Chunjie Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Dan Luo
- Department of Gastroenterology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430015, Wuhan, China
| | - Ting Wang
- The Center for Biomedical Research, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430100, China
| | - Yan Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhongyuan Tan
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Mingyuan Du
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, China
| | - Zhike He
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, China
| | - Hanzhong Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhenhua Zheng
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Yuan Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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23
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Wang J, Dou B, Zheng L, Cao W, Zeng X, Wen Y, Ma J, Li X. Synthesis of Na 2S 2O 4 mediated cleavable affinity tag for labeling of O-GlcNAc modified proteins via azide-alkyne cycloaddition. Bioorg Med Chem Lett 2021; 48:128244. [PMID: 34229054 DOI: 10.1016/j.bmcl.2021.128244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 01/22/2023]
Abstract
A facile and convergent procedure for the synthesis of azobenzene-based probe was reported, which could selectively release interested proteins conducted with sodium dithionite. Besides, the cleavage efficiency is closely associated with the structural features, in which an ortho-hydroxyl substituent is necessary for reactivity. In addition, the azobenzene tag applied in the Ac4GlcNAz-labled proteins demonstrated high efficiency and selectivity in comparison with Biotin-PEG4-Alkyne, which provides a useful platform for enrichment of any desired bioorthogonal proteomics.
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Affiliation(s)
- Jiajia Wang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medicine Science, Henan University, 475004 Kaifeng, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Biao Dou
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medicine Science, Henan University, 475004 Kaifeng, China
| | - Lu Zheng
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medicine Science, Henan University, 475004 Kaifeng, China
| | - Wei Cao
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medicine Science, Henan University, 475004 Kaifeng, China
| | - Xueke Zeng
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medicine Science, Henan University, 475004 Kaifeng, China
| | - Yinhang Wen
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medicine Science, Henan University, 475004 Kaifeng, China
| | - Jing Ma
- School of Pharmacy, Institute for Innovative Drug Design and Evaluation, Henan University, 475004 Kaifeng, China.
| | - Xia Li
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medicine Science, Henan University, 475004 Kaifeng, China.
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24
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Abstract
Mycobacteria, which cause tuberculosis and related diseases, possess a diverse set of complex envelope lipids that provide remarkable tolerance to antibiotics and are major virulence factors that drive pathogenesis. Recently, metabolic labeling and bio-orthogonal chemistry have been harnessed to develop chemical probes for tagging specific lipids in live mycobacteria, enabling a range of new basic and translational research avenues. A toolbox of probes has been developed for labeling mycolic acids and their derivatives, including trehalose-, arabinogalactan-, and protein-linked mycolates, as well as newer probes for labeling phthiocerol dimycocerosates (PDIMs) and potentially other envelope lipids. These lipid-centric tools have yielded fresh insights into mycobacterial growth and host interactions, provided new avenues for drug target discovery and characterization, and inspired innovative diagnostic and therapeutic strategies.
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Affiliation(s)
- Kyle J Biegas
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA
| | - Benjamin M Swarts
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA.
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25
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Trautwein-Schult A, Bartel J, Maaß S, Becher D. Metabolic Labeling of Clostridioides difficile Proteins. Methods Mol Biol 2021; 2228:271-82. [PMID: 33950497 DOI: 10.1007/978-1-0716-1024-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The introduction of stable isotopes in vivo via metabolic labeling approaches (SILAC or 15N-labeling) allows, after combination of differentially treated labeled and unlabeled cells or protein extracts, for correction of protein quantification errors implemented during elaborated sample preparation workflows. The SILAC-based approach uses heavy arginine and lysine to incorporate the label into bacterial strains and cell lines, whereas 15N-metabolic labeling is achieved by cultivation in 15N-salt containing media. In case of Clostridioides difficile, the lack in arginine and lysine auxotrophy as well as the Stickland dominated metabolism makes metabolic labeling challenging. Here, a step-by-step guideline for the metabolic labeling of C. difficile is described, which combines cultivation in liquid 15N-substituted medium followed by cultivation steps on solid 15N-substituted medium. The described procedure results in a label incorporation rate higher than 97%. Cells prepared by the following method can be used as standard for relative quantification approaches of, e.g., the membrane or surface proteome of C. difficile.
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26
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Han SS, Kang SW. Metabolic Labeling of Live Stem Cell for In Vitro Imaging and In Vivo Tracking. Methods Mol Biol 2020; 2150:153-66. [PMID: 30997638 DOI: 10.1007/7651_2019_224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Stem cell therapy offers promising solutions to diseases and injuries that traditional medicines and therapies can't effectively cure. To get and explain their full therapeutic potentials, the survival, viability, integration, homing, and differentiation of stem cells after transplant must be clearly understood. To meet these urgent needs, noninvasive stem cell imaging and tracking technologies have been developed. Metabolic labeling technique is one of the most powerful tools for live cell imaging and tracking. In addition, it has many advantages for in vivo live cell imaging and tracking such as low background, correlation of survival, and very toxic and nontoxic by-products. Herein, we described the fundamental information and process of metabolic labeling techniques and suggested optimal condition for in vitro and in vivo imaging and tracking of human umbilical cord blood-derived endothelial progenitor cells (hUCB-EPCs). Based on this study, metabolic labeling techniques can be helpful for understanding the safety and effectiveness of stem cell-based therapy and determining the utility of stem cells in downstream experiments.
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27
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Mattay J, Dittmar M, Rentmeister A. Chemoenzymatic strategies for RNA modification and labeling. Curr Opin Chem Biol 2021; 63:46-56. [PMID: 33690011 DOI: 10.1016/j.cbpa.2021.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/20/2021] [Accepted: 01/31/2021] [Indexed: 12/17/2022]
Abstract
RNA is a central molecule in numerous cellular processes, including transcription, translation, and regulation of gene expression. To reveal the numerous facets of RNA function and metabolism in cells, labeling has become indispensable and enables the visualization, isolation, characterization, and even quantification of certain RNA species. In this review, we will cover chemoenzymatic approaches for covalent RNA labeling. These approaches rely on an enzymatic step to introduce an RNA modification before conjugation with a label for detection or isolation. We start with in vitro manipulation of RNA, sorted according to the enzymatic reaction exploited. Then, metabolic approaches for co- and post-transcriptional RNA labeling will be treated. We focus on recent advances in the field and highlight the most relevant applications for cellular imaging, RNA isolation and sequencing.
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Affiliation(s)
- Johanna Mattay
- Department of Chemistry, Institute of Biochemistry, University of Münster, Correnstr. 36, 48149, Münster, Germany
| | - Maria Dittmar
- Department of Chemistry, Institute of Biochemistry, University of Münster, Correnstr. 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Correnstr. 36, 48149, Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, 48149, Münster, Germany.
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28
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Hou Z, Han X, Wang Z, Ghazanfar S, Yang J, Liu H. A terminal alkyne and disulfide functionalized agarose resin specifically enriches azidohomoalanine labeled nascent proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1165:122527. [PMID: 33486215 DOI: 10.1016/j.jchromb.2021.122527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/27/2020] [Accepted: 01/02/2021] [Indexed: 10/22/2022]
Abstract
Nascent proteome presents dynamic changes in response to a certain stimulus. Thus, monitoring nascent proteome is critical to uncovering the involved biological mechanism. But the low-abundance of nascent proteome against an overwhelming pre-existing proteome limits its identification and quantification. Herein, we present a novel strategy to enrich nascent proteome from whole cell lysate for further analysis by mass spectrometry. We employed a terminal alkyne and disulfide functionalized agarose resin to capture nascent proteome which had been labeled by L-azidohomoalanine. Results from the western blot, silver staining and pulse metabolic labeling suggested that the nascent proteome could be enriched efficiently. Applied to Hela cells, the method identified about 700 nascent proteins with good correlation with previous reports. The above indicates that our strategy can be used to reveal the proteome dynamics of biological processes.
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Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine & Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xiao Han
- Center for Mitochondrial Biology and Medicine & Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhen Wang
- Center for Mitochondrial Biology and Medicine & Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Sana Ghazanfar
- Center for Mitochondrial Biology and Medicine & Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jeffy Yang
- Schulich Medicine and Dentistry, Western University, London N6A3K7, Canada
| | - Huadong Liu
- Center for Mitochondrial Biology and Medicine & Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
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29
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Kotrys AV, Borowski LS, Szczesny RJ. High-Throughput Measurement of Mitochondrial RNA Turnover in Human Cultured Cells. Methods Mol Biol 2021; 2192:133-146. [PMID: 33230771 DOI: 10.1007/978-1-0716-0834-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
RNA turnover is an essential part of the gene expression pathway, and there are several experimental approaches for its determination. High-throughput measurement of global RNA turnover rates can provide valuable information about conditions or proteins that impact gene expression. Here, we present a protocol for mitochondrial RNA turnover analysis which involves metabolic labeling of RNA coupled with quantitative high-throughput fluorescent microscopy. This approach gives an excellent opportunity to discover new factors involved in mitochondrial gene regulation when combined with loss-of-function screening strategy.
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Affiliation(s)
- Anna V Kotrys
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Lukasz S Borowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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30
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Abstract
In recent decades, mass spectrometry has moved more than ever before into the front line of protein-centered research. After being established at the qualitative level, the more challenging question of quantification of proteins and peptides using mass spectrometry has become a focus for further development. In this chapter, we discuss and review actual strategies and problems of the methods for the quantitative analysis of peptides, proteins, and finally proteomes by mass spectrometry. The common themes, the differences, and the potential pitfalls of the main approaches are presented in order to provide a survey of the emerging field of quantitative, mass spectrometry-based proteomics.
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Affiliation(s)
- Svitlana Rozanova
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Medical Proteome Analysis, Center for protein diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany
| | - Katalin Barkovits
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Medical Proteome Analysis, Center for protein diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany
| | - Miroslav Nikolov
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany.,Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany.,Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany. .,Medical Proteome Analysis, Center for protein diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany.
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31
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Ancajas CF, Ricks TJ, Best MD. Metabolic labeling of glycerophospholipids via clickable analogs derivatized at the lipid headgroup. Chem Phys Lipids 2020; 232:104971. [PMID: 32898510 PMCID: PMC7606648 DOI: 10.1016/j.chemphyslip.2020.104971] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/01/2020] [Indexed: 02/09/2023]
Abstract
Metabolic labeling, in which substrate analogs containing diminutive tags can infiltrate biosynthetic pathways and generate labeled products in cells, has led to dramatic advancements in the means by which complex biomolecules can be detected and biological processes can be elucidated. Within this realm, metabolic labeling of lipid products, particularly in a manner that is headgroup-specific, brings about a number of technical challenges including the complexity of lipid metabolic pathways as well as the simplicity of biosynthetic precursors to headgroup functionality. As such, only a handful of strategies for metabolic labeling of lipids have thus far been reported. However, these approaches provide enticing examples of how strategic modifications to substrate structures, particularly by introducing clickable moieties, can enable the hijacking of lipid biosynthesis. Furthermore, early work in this field has led to an explosion in diverse applications by which these techniques have been exploited to answer key biological questions or detect and track various lipid-containing biological entities. In this article, we review these efforts and emphasize recent advancements in the development and application of lipid metabolic labeling strategies.
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Affiliation(s)
- Christelle F Ancajas
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Tanei J Ricks
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Michael D Best
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA.
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32
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Tera M, Luedtke NW. Cross-linking cellular nucleic acids via a target-directing double click reagent. Methods Enzymol 2020; 641:433-457. [PMID: 32713534 DOI: 10.1016/bs.mie.2020.04.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bioorthogonal ligation reactions are powerful tools for characterizing DNA metabolism, DNA-protein binding interactions, and they even provide new leads for therapeutic strategies. Nucleoside analogs can deliver bioorthogonal functional groups into chromatin via cellular metabolic pathways, however, insufficient phosphorylation by endogenous kinases often limits the efficiency of their incorporation. Even when successfully metabolized into biopolymers, steric hindrance of the modified nucleotide by chromatin can inhibit subsequent click reactions. In this chapter, we describe methods that overcome these limitations. Nucleotide monophosphate triesterers can bypass the need for cellular nucleoside kinase activity and thereby enable efficient incorporation of azide groups into cellular DNA. Steric access to and modification of the azide groups within natively folded chromatin can then be accomplished using a bioorthogonal "intercalating reagent" comprised of a cationic Sondheimer diyne that reversibly intercalates into duplexes where it undergoes tandem, strain-promoted cross-linking of two azides to give DNA-DNA interstrand crosslinks or DNA-fluorophore conjugation, depending on the relative number and spatial orientation of the azide groups in the DNA.
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Affiliation(s)
- Masayuki Tera
- Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan.
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33
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Penner N, Purushothama S, Pepinsky B. Tissue distribution of 35S-metabolically labeled neublastin (BG00010) in rats. J Pharm Biomed Anal 2020; 184:113154. [PMID: 32097771 DOI: 10.1016/j.jpba.2020.113154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 11/20/2022]
Abstract
Neublastin (NBN) is a neurotrophic growth factor that promotes the survival and regenerative properties of nociceptive neurons and has been tested in clinical trials as a treatment for neuropathic pain in individuals with sciatica and painful lumbosacral radiculopathy. Like many low molecular weight heparin binding proteins, NBN is rapidly cleared from the blood following systemic administration. To explore ADME properties of NBN in rats, we used metabolically 35S-labeled NBN following IV and SC administration quantifying counts and intact protein in kidney, liver, brain, serum, and urine at 5 min, 8 h, 24 h and 48 h, and biodistribution in whole body carcasses by QWBA at 2, 8, 48, 96, and 168 h post dose. NBN is rapidly taken up by tissues mainly by liver and kidney and then degraded. Products of degradation are excreted in urine or recycled and utilized for resynthesis. The data we generated for NBN provides a first look at the complex clearance mechanisms for this protein and should aid in the design of ADME studies for other heparin binding proteins.
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34
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Skidmore AM, Adcock RS, Jonsson CB, Golden JE, Chung DH. Benzamidine ML336 inhibits plus and minus strand RNA synthesis of Venezuelan equine encephalitis virus without affecting host RNA production. Antiviral Res 2020; 174:104674. [PMID: 31816348 PMCID: PMC6935354 DOI: 10.1016/j.antiviral.2019.104674] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/27/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022]
Abstract
Venezuelan equine encephalitis virus (VEEV) is an alphavirus that is endemic to the Americas. VEEV outbreaks occur periodically and cause encephalitis in both humans and equids. There are currently no therapeutics or vaccines for treatment of VEEV in humans. Our group has previously reported on the development of a benzamidine VEEV inhibitor, ML336, which shows potent antiviral activity in both in vitro and in vivo models of infection. In cell culture experiments, ML336 inhibits viral RNA synthesis when added 2-4 h post-infection, and mutations conferring resistance occur within the viral nonstructural proteins (nsP2 and nsP4). We hypothesized that ML336 targets an activity of the viral replicase complex and inhibits viral RNA synthesis. To test this hypothesis, we employed various biochemical and cellular assays. Using structural analogues of ML336, we demonstrate that the cellular antiviral activity of these compounds correlates with their inhibition of viral RNA synthesis. For instance, the IC50 of ML336 for VEEV RNA synthesis inhibition was determined as 1.1 nM, indicating potent anti-RNA synthesis activity in the low nanomolar range. While ML336 efficiently inhibited VEEV RNA synthesis, a much weaker effect was observed against the Old World alphavirus Chikungunya virus (IC50 > 4 μM), agreeing with previous data from a cell based assay. Using a tritium incorporation assay, we demonstrated that there was no significant inhibition of cellular transcription. With a combination of fluorography, strand-specific qRT-PCR, and tritium incorporation, we demonstrated that ML336 inhibits the synthesis of the positive sense genomic, negative sense template, and subgenomic RNAs of VEEV. Based on these results, we propose that the mechanism of action for this class of antiviral compounds is inhibition of viral RNA synthesis through interaction with the viral replicase complex.
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Affiliation(s)
- Andrew M Skidmore
- Department of Microbiology and Immunology, University of Louisville, 505 South Hancock St, Room 642 C, Louisville, KY, USA.
| | - Robert S Adcock
- Center of Predictive Medicine, University of Louisville, 505 South Hancock St, Room 617, Louisville, KY, USA.
| | - Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Ave, Room 810 B, Memphis, TN, USA.
| | - Jennifer E Golden
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Dr, Room 7123, Madison, WI, USA.
| | - Dong-Hoon Chung
- Department of Microbiology and Immunology, University of Louisville, 505 South Hancock St, Room 642 C, Louisville, KY, USA; Center of Predictive Medicine, University of Louisville, 505 South Hancock St, Room 617, Louisville, KY, USA.
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35
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Abstract
The amount of a protein that is made in a cell is determined not only by the corresponding mRNA level but also by the efficiency with which the mRNA is translated. Very powerful transcriptome-wide methods are available to analyze both the density of ribosomes on each mRNA and the rate at which polypeptides are elongated. However, for many research questions, simpler, less expensive methods are more suitable. Here we describe two methods to assess the general translation status of cells: polysome profiling by sucrose density gradient centrifugation and metabolic labeling using radioactive amino acids. Both methods can also be used to examine translation of individual mRNAs.
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Affiliation(s)
- Kathrin Bajak
- Deutsche Krebsforschungszentrum (DKF), Heidelberg, Germany
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36
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Abstract
Inositol phosphate (IP) and phosphatidylinositol (PI) signaling are critical signal transduction pathways responsible for generating numerous receptor-mediated cellular responses. Biochemical and genetic studies have revealed diverse roles of IP and PI signaling in eukaryotic signaling, but detailed characterization of unique IP and PI signaling profiles in response to different agonists and among cell types remains largely unexplored. Here, we outline steady-state inositol metabolic-labeling techniques that can be leveraged to assess the IP and PI signaling state in eukaryotic cells. This flexible technique can be amended and optimized to your cell line of interest, perturbed with biochemical, genetic, or pharmacological alteration, and used to provide comprehensive inositol profiling in various cellular systems.
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37
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Lusser A, Gasser C, Trixl L, Piatti P, Delazer I, Rieder D, Bashin J, Riml C, Amort T, Micura R. Thiouridine-to-Cytidine Conversion Sequencing (TUC-Seq) to Measure mRNA Transcription and Degradation Rates. Methods Mol Biol 2020; 2062:191-211. [PMID: 31768978 DOI: 10.1007/978-1-4939-9822-7_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The study of RNA dynamics, specifically RNA transcription and decay rates, has gained increasing attention in recent years because various mechanisms have been discovered that affect mRNA half-life, thereby ultimately controlling protein output. Therefore, there is a need for methods enabling minimally invasive, simple and high-throughput determination of RNA stability that can be applied to determine RNA transcription and decay rates in cells and organisms. We have recently developed a protocol which we named TUC-seq to directly distinguish newly synthesized transcripts from the preexisting pool of transcripts by metabolic labeling of nascent RNAs with 4-thiouridine (4sU) followed by osmium tetroxide-mediated conversion of 4sU to cytidine (C) and direct sequencing. In contrast to other related methods (SLAM-seq, TimeLapse-seq), TUC-seq converts 4sU to a native C instead of an alkylated or otherwise modified nucleoside derivative. TUC-seq can be applied to any cell type that is amenable to 4sU labeling. By employing different labeling strategies (pulse or pulse-chase labeling), it is suitable for a broad field of applications and provides a fast and highly efficient means to determine mRNA transcription and decay rates.
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Affiliation(s)
- Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
| | - Catherina Gasser
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, Leopold Franzens University, Innsbruck, Austria
| | - Lukas Trixl
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Isabel Delazer
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Christian Riml
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, Leopold Franzens University, Innsbruck, Austria
| | - Thomas Amort
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Ronald Micura
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, Leopold Franzens University, Innsbruck, Austria.
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38
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Abstract
It is well established that palmitoylation plays a key role in the regulation of immune checkpoints, but the technical challenges in detecting protein palmitoylation have significantly prohibited further researches in this field. Till now, different approaches have been proposed, such as mutagenesis, antibody-based methods, bioinformatic prediction, "palmitate-centric" approaches, and "cysteine-centric" approaches. Of specific importance, high-throughput methods that allow the unbiased discovery of palmitoylation in the whole proteome should be further improved and employed. This chapter will summarize the methodological progresses for detecting protein palmitoylation, aiming to facilitate future researches in the lipid modification of immune checkpoint proteins.
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Affiliation(s)
- Haojie Lu
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200438, China.
| | - Caiyun Fang
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200438, China
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39
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Sun F, Wu R. Systematic and site-specific analysis of N-glycoproteins on the cell surface by integrating bioorthogonal chemistry and MS-based proteomics. Methods Enzymol 2019; 626:223-247. [PMID: 31606076 DOI: 10.1016/bs.mie.2019.06.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Glycoproteins on the cell surface are essential for various cellular activities including cell-cell communication and cell-matrix interaction. Alterations of glycosylation are correlated with many diseases such as cancer and infectious diseases. However, it is greatly challenging to systematically and site-specially analyze glycoproteins only located on cell surface because of the heterogeneity of glycans, the low abundance of many surface glycoproteins and the requirement of effective methods to separate surface glycoproteins. In this chapter, we briefly review existing mass spectrometry (MS)-based methods for global analysis of surface glycoproteins. Then we discuss an effective method integrating metabolic labeling, click and enzymatic reactions, and MS-based proteomics to comprehensively and site-specifically investigate cell surface N-glycoproteins. A detailed protocol for this method is also included. In combination with quantitative proteomics, we applied this method to quantify cell surface N-glycoproteins and study the relationship between cell invasiveness and N-sialoglycoproteins on the cell surface. Considering the importance of surface glycoproteins, this method can be extensively applied to advance glycoscience, which leads to a better understanding of the molecular mechanisms of human diseases, and the discovery of surface glycoproteins as biomarkers for disease detection.
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Affiliation(s)
- Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, United States.
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40
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Cheung See Kit M, Martin BR. Enrichment of S-Palmitoylated Proteins for Mass Spectrometry Analysis. Methods Mol Biol 2019; 2009:71-9. [PMID: 31152396 DOI: 10.1007/978-1-4939-9532-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
As the 10-year anniversary of their first introduction approaches, alkynyl fatty acids have revolutionized the analysis of S-palmitoylation dynamics, acting as functional mimics incorporated into native modification sites in cultured cells. The alkyne functional group provides a robust handle for bioorthogonal Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) to reporter-linked azides, forming a stable conjugate for enrichment for mass spectrometry analysis or in-gel fluorescence. Importantly, metabolic labeling enables time-dependent analysis of S-palmitoylation dynamics, which can be used to profile incorporation and turnover rates across the proteome. Here we present a protocol for cell labeling, click chemistry conjugation, enrichment, and isobaric tandem mass tag labeling for quantitative mass spectrometry analysis of protein S-palmitoylation.
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41
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Saleh AM, Wilding KM, Calve S, Bundy BC, Kinzer-Ursem TL. Non-canonical amino acid labeling in proteomics and biotechnology. J Biol Eng 2019; 13:43. [PMID: 31139251 PMCID: PMC6529998 DOI: 10.1186/s13036-019-0166-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/11/2019] [Indexed: 02/03/2023] Open
Abstract
Metabolic labeling of proteins with non-canonical amino acids (ncAAs) provides unique bioorthogonal chemical groups during de novo synthesis by taking advantage of both endogenous and heterologous protein synthesis machineries. Labeled proteins can then be selectively conjugated to fluorophores, affinity reagents, peptides, polymers, nanoparticles or surfaces for a wide variety of downstream applications in proteomics and biotechnology. In this review, we focus on techniques in which proteins are residue- and site-specifically labeled with ncAAs containing bioorthogonal handles. These ncAA-labeled proteins are: readily enriched from cells and tissues for identification via mass spectrometry-based proteomic analysis; selectively purified for downstream biotechnology applications; or labeled with fluorophores for in situ analysis. To facilitate the wider use of these techniques, we provide decision trees to help guide the design of future experiments. It is expected that the use of ncAA labeling will continue to expand into new application areas where spatial and temporal analysis of proteome dynamics and engineering new chemistries and new function into proteins are desired.
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Affiliation(s)
- Aya M. Saleh
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN USA
| | - Kristen M. Wilding
- Department of Chemical Engineering, Brigham Young University, Provo, UT USA
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN USA
| | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT USA
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42
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Abstract
Proteins can be radiolabeled either during synthesis, typically using 35S-cysteine/methionine (35S-Cys/Met), or after synthesis, by adding a radiolabeled posttranslational modification. Here we describe how protein S-palmitoylation, and its dynamics, can be monitored by 3H-palmitate labeling and how the importance of S-palmitoylation in protein biogenesis and turnover can be investigated using 35S-Cys/Met pulse-chase metabolic labeling. Proteins frequently have multiple palmitoylation sites. The importance thereof on the design and interpretation of metabolic labeling experiments is discussed.
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Affiliation(s)
- Laurence Abrami
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Robin A Denhardt-Eriksson
- Global Health Institute, Laboratory of Computational Systems Biotechnology, EPFL, Lausanne, Switzerland
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43
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Abstract
Stable isotope probing combined with metaproteomics enables the detection and characterization of active key species in microbial populations under near-natural conditions, which greatly helps to understand the metabolic functions of complex microbial communities. This is achieved by providing growth substrates labeled with heavy isotopes such as 13C, which will be assimilated into microbial biomass. After subsequent extraction of proteins and proteolytic cleavage into peptides, the heavy isotope enrichment can be detected by high-resolution mass spectrometric analysis, and linked to the functional and taxonomic characterization of these biomarkers. Here we provide protocols for obtaining isotopically labeled proteins and for downstream SIP-metaproteomics analysis.
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Affiliation(s)
- Martin Taubert
- Faculty of Biological Sciences, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.
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44
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Abstract
Experimental protocols for the synthesis and secretion of proteoglycans in cell culture models are important to study specific biosynthetic steps or disorders in which a defect in proteoglycans is expected. We describe a method using 35S-sulfate to metabolically label newly synthesized proteoglycans from cell cultures in order to measure proteoglycan synthesis and secretion. The method is set up for fibroblast and chondrocyte cultures, but can be extended to other cell types.
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Affiliation(s)
- Chiara Paganini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Rossella Costantini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Antonio Rossi
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy.
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45
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Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
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Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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46
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Schmid M, Tudek A, Jensen TH. Preparation of RNA 3' End Sequencing Libraries of Total and 4-thiouracil Labeled RNA for Simultaneous Measurement of Transcription, RNA Synthesis and Decay in S. cerevisiae. Bio Protoc 2019; 9:e3189. [PMID: 30931349 DOI: 10.21769/bioprotoc.3189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Cellular RNA levels are determined by the rates of RNA transcription from the gene template and subsequent RNA stability. Knowledge about both transcription and RNA decay is, therefore, necessary to interpret RNA levels and gene expression, especially during cellular processes where these parameters change. Numerous experimental strategies have been developed to measure transcription and RNA decay rates. However, to our knowledge, none of those techniques can simultaneously interrogate transcription and RNA decay. The presented protocol allows this and provides a simple approach to simultaneously estimate total RNA levels, transcription and decay rates from the same RNA sample. It is based on brief metabolic labeling of RNA and subsequent concurrent sequencing of polyA+ and polyA- RNA 3' ends. The protocol was developed in S. cerevisiae and should be broadly applicable.
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Affiliation(s)
- Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Agnieszka Tudek
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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47
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Abstract
Protein prenylation, found in eukaryotes, is a posttranslational modification in which one or two isoprenoid groups are added to the C terminus of selected proteins using either a farnesyl group or a geranylgeranyl group. Prenylation facilitates protein localization mainly to the plasma membrane where the prenylated proteins, including small GTPases, mediate signal transduction pathways. Changes in the level of prenylated proteins may serve a critical function in a variety of diseases. Metabolic labeling using modified isoprenoid probes followed by enrichment and proteomic analysis allows the identities and levels of prenylated proteins to be investigated. In this protocol, we illustrate how the conditions for metabolic labeling are optimized to maximize probe incorporation in HeLa cells through a combination of in-gel fluorescence and densitometric analysis.
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Affiliation(s)
- Mina Ahmadi
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
| | | | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA.
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48
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Wolfe MB, Goldstrohm AC, Freddolino PL. Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing. Methods 2019; 155:88-103. [PMID: 30529548 DOI: 10.1016/j.ymeth.2018.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 11/21/2022] Open
Abstract
Many open questions in RNA biology relate to the kinetics of gene expression and the impact of RNA binding regulatory factors on processing or decay rates of particular transcripts. Steady state measurements of RNA abundance obtained from RNA-seq approaches are not able to separate the effects of transcription from those of RNA decay in the overall abundance of any given transcript, instead only giving information on the (presumed steady-state) abundances of transcripts. Through the combination of metabolic labeling and high-throughput sequencing, several groups have been able to measure both transcription rates and decay rates of the entire transcriptome of an organism in a single experiment. This review focuses on the methodology used to specifically measure RNA decay at a global level. By comparing and contrasting approaches and describing the experimental protocols in a modular manner, we intend to provide both experienced and new researchers to the field the ability to combine aspects of various protocols to fit the unique needs of biological questions not addressed by current methods.
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49
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Yu A, Zhao J, Peng W, Banazadeh A, Williamson SD, Goli M, Huang Y, Mechref Y. Advances in mass spectrometry-based glycoproteomics. Electrophoresis 2018; 39:3104-3122. [PMID: 30203847 PMCID: PMC6375712 DOI: 10.1002/elps.201800272] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/03/2018] [Accepted: 09/03/2018] [Indexed: 12/13/2022]
Abstract
Protein glycosylation, an important PTM, plays an essential role in a wide range of biological processes such as immune response, intercellular signaling, inflammation, and host-pathogen interaction. Aberrant glycosylation has been correlated with various diseases. However, studying protein glycosylation remains challenging because of low abundance, microheterogeneities of glycosylation sites, and poor ionization efficiency of glycopeptides. Therefore, the development of sensitive and accurate approaches to characterize protein glycosylation is crucial. The identification and characterization of protein glycosylation by MS is referred to as the field of glycoproteomics. Methods such as enrichment, metabolic labeling, and derivatization of glycopeptides in conjunction with different MS techniques and bioinformatics tools, have been developed to achieve an unequivocal quantitative and qualitative characterization of glycoproteins. This review summarizes the recent developments in the field of glycoproteomics over the past 6 years (2012 to 2018).
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Affiliation(s)
- Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Seth D Williamson
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
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50
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Ren X, Evangelista-Leite D, Wu T, Rajab TK, Moser PT, Kitano K, Economopoulos KP, Gorman DE, Bloom JP, Tan JJ, Gilpin SE, Zhou H, Mathisen DJ, Ott HC. Metabolic glycan labeling and chemoselective functionalization of native biomaterials. Biomaterials 2018; 182:127-34. [PMID: 30118980 DOI: 10.1016/j.biomaterials.2018.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 01/01/2023]
Abstract
Decellularized native extracellular matrix (ECM) biomaterials are widely used in tissue engineering and have reached clinical application as biomesh implants. To enhance their regenerative properties and postimplantation performance, ECM biomaterials could be functionalized via immobilization of bioactive molecules. To facilitate ECM functionalization, we developed a metabolic glycan labeling approach using physiologic pathways to covalently incorporate click-reactive azide ligands into the native ECM of a wide variety of rodent tissues and organs in vivo, and into the ECM of isolated rodent and porcine lungs cultured ex vivo. The incorporated azides within the ECM were preserved after decellularization and served as chemoselective ligands for subsequent bioconjugation via click chemistry. As proof of principle, we generated alkyne-modified heparin, immobilized it onto azide-incorporated acellular lungs, and demonstrated its bioactivity by Antithrombin III immobilization and Factor Xa inhibition. The herein reported metabolic glycan labeling approach represents a novel platform technology for manufacturing click-reactive native ECM biomaterials, thereby enabling efficient and chemoselective functionalization of these materials to facilitate tissue regeneration and repair.
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