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Yazdanbakhsh M, Acker JP. Advancing in vivo assessment of red blood cell transfusions: A call for radiation-free methods in transfusion medicine. Transfus Apher Sci 2024:103928. [PMID: 38653627 DOI: 10.1016/j.transci.2024.103928] [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: 04/25/2024]
Abstract
RBC transfusions are a vital clinical therapy to treat anemic patients. The in vivo assessment of red blood cell (RBC) quality post-transfusion is critical to ensuring that the introduction of new RBC products meet established regulatory and clinical quality requirements. Although in vitro quality control testing is routinely performed by blood manufacturers, it is crucial that in vivo tests are performed during the evaluation and regulatory process of new RBC products. This article reviews existing in vivo techniques, like chromium-51 labelling and biotinylation, for determining the circulation and survival of RBCs, and advocates for a move to radiation-free methods. The timely need for radiation-free methods to assess emerging non-DEHP container systems is just one example of why efforts to improve the methods available for in vivo quality assessment is important in transfusion medicine. This review aims to advance our understanding of RBC transfusion in vivo quality assessment and enhance transfusion practices.
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Affiliation(s)
- Mahsa Yazdanbakhsh
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; Innovation and Portfolio Management, Canadian Blood Services, Edmonton, Alberta, Canada
| | - Jason P Acker
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; Innovation and Portfolio Management, Canadian Blood Services, Edmonton, Alberta, Canada.
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2
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Sarihan M, Kasap M, Akpinar G. Streamlined Biotinylation, Enrichment and Analysis for Enhanced Plasma Membrane Protein Identification Using TurboID and TurboID-Start Biotin Ligases. J Membr Biol 2024; 257:91-105. [PMID: 38289568 DOI: 10.1007/s00232-023-00303-y] [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: 11/03/2023] [Accepted: 12/23/2023] [Indexed: 04/11/2024]
Abstract
Plasma membrane proteins (PMPs) play pivotal roles in various cellular events and are crucial in disease pathogenesis, making their comprehensive characterization vital for biomedical research. However, the hydrophobic nature and low expression levels of PMPs pose challenges for conventional enrichment methods, hindering their identification and functional profiling. In this study, we presented a novel TurboID-based enrichment approach for PMPs that helped overcoming some of the existing limitations. We evaluated the efficacy of TurboID and its modified form, TurboID-START, in PMP enrichment, achieving efficient and targeted labelling of PMPs without the need for stable cell line generation. This approach resulted reduction in non-specific biotinylation events, leading to improved PMP enrichment and enabled assessment of the subcellular proteome associated with the plasma membrane. Our findings paved the way for studies targeting the dynamic nature of the plasma membrane proteome and aiming to capture transient associations of proteins with the plasma membrane. The novel TurboID-based enrichment approach presented here offers promising prospects for in-depth investigations into PMPs and their roles in cellular processes.
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Affiliation(s)
- Mehmet Sarihan
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical School, 41001, Umuttepe, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical School, 41001, Umuttepe, Kocaeli, Turkey.
| | - Gurler Akpinar
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical School, 41001, Umuttepe, Kocaeli, Turkey
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3
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Remy O, Santin YG. Identification of Protein Partners by APEX2 Proximity Labeling. Methods Mol Biol 2024; 2715:321-329. [PMID: 37930538 DOI: 10.1007/978-1-0716-3445-5_21] [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
Proximity labeling methods enable the identification of proteins in the vicinity of a protein of interest in living cells. Among them, APEX2 proximity is a powerful method to spatiotemporally define in vivo "proxisomes" in dynamic bacterial protein systems. Here we describe a standardized APEX2 proximity labeling protocol and possible adaptations to capture protein partners in native conditions.
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4
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Li Y, Zhang Y, Dinesh-Kumar SP. TurboID-Based Proximity Labeling: A Method to Decipher Protein-Protein Interactions in Plants. Methods Mol Biol 2024; 2724:257-272. [PMID: 37987912 DOI: 10.1007/978-1-0716-3485-1_19] [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: 11/22/2023]
Abstract
Proteins form complex networks through interaction to drive biological processes. Thus, dissecting protein-protein interactions (PPIs) is essential for interpreting cellular processes. To overcome the drawbacks of traditional approaches for analyzing PPIs, enzyme-catalyzed proximity labeling (PL) techniques based on peroxidases or biotin ligases have been developed and successfully utilized in mammalian systems. However, the use of toxic H2O2 in peroxidase-based PL, the requirement of long incubation time (16-24 h), and higher incubation temperature (37 °C) with biotin in BioID-based PL significantly restricted their applications in plants. TurboID-based PL, a recently developed approach, circumvents the limitations of these methods by providing rapid PL of proteins under room temperature. We recently optimized the use of TurboID-based PL in plants and demonstrated that it performs better than BioID in labeling endogenous proteins. Here, we describe a step-by-step protocol for TurboID-based PL in studying PPIs in planta, including Agrobacterium-based transient expression of proteins, biotin treatment, protein extraction, removal of free biotin, quantification, and enrichment of the biotinylated proteins by affinity purification. We describe the PL using plant viral immune receptor N, which belongs to the nucleotide-binding leucine-rich repeat (NLR) class of immune receptors, as a model. The method described could be easily adapted to study PPI networks of other proteins in Nicotiana benthamiana and provides valuable information for future application of TurboID-based PL in other plant species.
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Affiliation(s)
- Yuanyuan Li
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA.
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5
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Konovalova A. Components Subcellular Localization: Cell Surface Exposure. Methods Mol Biol 2024; 2715:99-110. [PMID: 37930524 DOI: 10.1007/978-1-0716-3445-5_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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Surface-exposed proteins of Gram-negative bacteria are represented by integral outer membrane β-barrel proteins and lipoproteins. There are no computational methods to predict surface-exposed lipoproteins, and therefore lipoprotein topology must be experimentally tested. This chapter describes several distinct but complementary methods for detection of surface-exposed proteins: cell surface protein labeling, accessibility to extracellular protease or antibodies, and SpyTag/SpyCatcher system.
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Affiliation(s)
- Anna Konovalova
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA.
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6
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Garapati K, Ding H, Charlesworth MC, Kim Y, Zenka R, Saraswat M, Mun DG, Chavan S, Shingade A, Lucien F, Zhong J, Kandasamy RK, Pandey A. sBioSITe enables sensitive identification of the cell surface proteome through direct enrichment of biotinylated peptides. Clin Proteomics 2023; 20:56. [PMID: 38053024 PMCID: PMC10696767 DOI: 10.1186/s12014-023-09445-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Cell surface proteins perform critical functions related to immune response, signal transduction, cell-cell interactions, and cell migration. Expression of specific cell surface proteins can determine cell-type identity, and can be altered in diseases including infections, cancer and genetic disorders. Identification of the cell surface proteome remains a challenge despite several enrichment methods exploiting their biochemical and biophysical properties. METHODS Here, we report a novel method for enrichment of proteins localized to cell surface. We developed this new approach designated surface Biotinylation Site Identification Technology (sBioSITe) by adapting our previously published method for direct identification of biotinylated peptides. In this strategy, the primary amine groups of lysines on proteins on the surface of live cells are first labeled with biotin, and subsequently, biotinylated peptides are enriched by anti-biotin antibodies and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS By direct detection of biotinylated lysines from PC-3, a prostate cancer cell line, using sBioSITe, we identified 5851 peptides biotinylated on the cell surface that were derived from 1409 proteins. Of these proteins, 533 were previously shown or predicted to be localized to the cell surface or secreted extracellularly. Several of the identified cell surface markers have known associations with prostate cancer and metastasis including CD59, 4F2 cell-surface antigen heavy chain (SLC3A2) and adhesion G protein-coupled receptor E5 (CD97). Importantly, we identified several biotinylated peptides derived from plectin and nucleolin, both of which are not annotated in surface proteome databases but have been shown to have aberrant surface localization in certain cancers highlighting the utility of this method. CONCLUSIONS Detection of biotinylation sites on cell surface proteins using sBioSITe provides a reliable method for identifying cell surface proteins. This strategy complements existing methods for detection of cell surface expressed proteins especially in discovery-based proteomics approaches.
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Affiliation(s)
- Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Husheng Ding
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Yohan Kim
- Department of Urology, Mayo Clinic, Rochester, MN, USA
| | - Roman Zenka
- Proteomics Core, Mayo Clinic, Rochester, MN, USA
| | - Mayank Saraswat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Dong-Gi Mun
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Sandip Chavan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ashish Shingade
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Fabrice Lucien
- Department of Urology, Mayo Clinic, Rochester, MN, USA
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Jun Zhong
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Richard K Kandasamy
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
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7
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Murillo A, Holgado M, Laguna M. Reports on the sensitivity enhancement in interferometric based biosensors by biotin-streptavidin system. Heliyon 2023; 9:e23123. [PMID: 38149195 PMCID: PMC10750048 DOI: 10.1016/j.heliyon.2023.e23123] [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: 09/08/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
Antibody biotinylation is a process of attaching biotin molecules to antibodies by chemically modifying specific functional groups on the antibodies without altering their antigen recognition specificity. Biotin, a small vitamin, forms a strong and specific interaction with the protein streptavidin, resulting in a stable biotin-streptavidin (biotin-STV) complex. This biotin-STV interaction is widely exploited in various biotechnological applications, including biosensors. Biosensors are analytical devices that employ biological recognition elements, such as antibodies, enzymes, or nucleic acids, to detect and quantify target analytes in a sample. Antibodies are commonly used as recognition elements in biosensors due to their high specificity and affinity. In this study, the antibody anti-Bovine Serum Albumin (αBSA) has been biotinylated at different antibody:biotin ratios, and the stability of this labeling over time has been investigated. Furthermore, the sensitivity of the biosensor for detecting the Bovine Serum Albumin (BSA) protein has been compared using the biotinylated antibody and the non-biotinylated form, showing a four-fold improvement in detection. This system was also compared with the Enzyme-Linked ImmunoSorbent Assay (ELISA) technique. The advantages of using biotinylated antibodies in biosensors include increased stability and reproducibility of the biorecognition layer, as well as flexibility in sensor design, as different biotinylated antibodies can be utilized for diverse target analytes without altering the sensor's architecture.
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Affiliation(s)
- A.M.M. Murillo
- Group of Optics, Photonics, and Biophotonics, Center for Biomedical Technology (CTB), Universidad Politécnica de Madrid, Parque Científico y Tecnológico de La UPM, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos, IdISSC, C/Profesor Martín Lagos s/n, 4a Planta Sur, 28040, Madrid, Spain
| | - M. Holgado
- Group of Optics, Photonics, and Biophotonics, Center for Biomedical Technology (CTB), Universidad Politécnica de Madrid, Parque Científico y Tecnológico de La UPM, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos, IdISSC, C/Profesor Martín Lagos s/n, 4a Planta Sur, 28040, Madrid, Spain
- Department of Applied Physics and Materials Engineering, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, C/José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - M. Laguna
- Group of Optics, Photonics, and Biophotonics, Center for Biomedical Technology (CTB), Universidad Politécnica de Madrid, Parque Científico y Tecnológico de La UPM, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos, IdISSC, C/Profesor Martín Lagos s/n, 4a Planta Sur, 28040, Madrid, Spain
- Department of Applied Physics and Materials Engineering, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, C/José Gutiérrez Abascal, 2, 28006, Madrid, Spain
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8
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McKenney KM, Connacher RP, Dunshee EB, Goldstrohm AC. Chemi-Northern: a versatile chemiluminescent northern blot method for analysis and quantitation of RNA molecules. bioRxiv 2023:2023.10.10.561763. [PMID: 37873431 PMCID: PMC10592733 DOI: 10.1101/2023.10.10.561763] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
This report describes a chemiluminescence-based detection method for RNAs on northern blots, designated Chemi-Northern. This approach builds on the simplicity and versatility of northern blotting, while dispensing of the need for expensive and cumbersome radioactivity. RNAs are first separated on denaturing gel electrophoresis, transferred to a nylon membrane, and then hybridized to a biotinylated RNA or DNA antisense probe. Streptavidin conjugated with horseradish peroxidase and enhanced chemiluminescence substrate are then used to detect the probe bound to the target RNA. Our results demonstrate the versatility of this method in detecting natural and engineered RNAs expressed in cells, including messenger and noncoding RNAs. We show that Chemi-Northern detection is sensitive and fast, detecting attomole amounts of RNA in as little as 1 second, with high signal intensity and low background. The dynamic response displays excellent linearity. Using Chemi-Northern, we measure the significant, reproducible reduction of mRNA levels by human sequence-specific RNA-binding proteins, PUM1 and PUM2. Additionally, we measure the interaction of endogenous poly(A) binding protein, PABPC1, with poly-adenylated mRNA. Thus, the Chemi-Northern method provides a versatile, simple, cost-effective method to enable researchers to detect and measure changes in RNA expression, processing, binding, and decay of RNAs.
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Affiliation(s)
- Katherine M. McKenney
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert P. Connacher
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Elise B. Dunshee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aaron C. Goldstrohm
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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9
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Sarhadi TR, Panse JS, Nagotu S. Mind the gap: Methods to study membrane contact sites. Exp Cell Res 2023; 431:113756. [PMID: 37633408 DOI: 10.1016/j.yexcr.2023.113756] [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: 03/28/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/28/2023]
Abstract
Organelles are dynamic entities whose functions are essential for the optimum functioning of cells. It is now known that the juxtaposition of organellar membranes is essential for the exchange of metabolites and their communication. These functional apposition sites are termed membrane contact sites. Dynamic membrane contact sites between various sub-cellular structures such as mitochondria, endoplasmic reticulum, peroxisomes, Golgi apparatus, lysosomes, lipid droplets, plasma membrane, endosomes, etc. have been reported in various model systems. The burgeoning area of research on membrane contact sites has witnessed several manuscripts in recent years that identified the contact sites and components involved. Several methods have been developed to identify, measure and analyze the membrane contact sites. In this manuscript, we aim to discuss important methods developed to date that are used to study membrane contact sites.
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Affiliation(s)
- Tanveera Rounaque Sarhadi
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Janhavee Shirish Panse
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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10
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Radford RAW, Rayner SL, Szwaja P, Morsch M, Cheng F, Zhu T, Widagdo J, Anggono V, Pountney DL, Chung R, Lee A. Identification of phosphorylated tau protein interactors in progressive supranuclear palsy (PSP) reveals networks involved in protein degradation, stress response, cytoskeletal dynamics, metabolic processes, and neurotransmission. J Neurochem 2023; 165:563-586. [PMID: 36847488 PMCID: PMC10953353 DOI: 10.1111/jnc.15796] [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: 11/23/2022] [Revised: 01/27/2023] [Accepted: 02/21/2023] [Indexed: 03/01/2023]
Abstract
Progressive supranuclear palsy (PSP) is a late-onset neurodegenerative disease defined pathologically by the presence of insoluble phosphorylated-Tau (p-Tau) in neurons and glia. Identifying co-aggregating proteins within p-Tau inclusions may reveal important insights into processes affected by the aggregation of Tau. We used a proteomic approach, which combines antibody-mediated biotinylation and mass spectrometry (MS) to identify proteins proximal to p-Tau in PSP. Using this proof-of-concept workflow for identifying interacting proteins of interest, we characterized proteins proximal to p-Tau in PSP cases, identifying >84% of previously identified interaction partners of Tau and known modifiers of Tau aggregation, while 19 novel proteins not previously found associated with Tau were identified. Furthermore, our data also identified confidently assigned phosphorylation sites that have been previously reported on p-Tau. Additionally, using ingenuity pathway analysis (IPA) and human RNA-seq datasets, we identified proteins previously associated with neurological disorders and pathways involved in protein degradation, stress responses, cytoskeletal dynamics, metabolism, and neurotransmission. Together, our study demonstrates the utility of biotinylation by antibody recognition (BAR) approach to answer a fundamental question to rapidly identify proteins in proximity to p-Tau from post-mortem tissue. The application of this workflow opens up the opportunity to identify novel protein targets to give us insight into the biological process at the onset and progression of tauopathies.
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Affiliation(s)
- Rowan A. W. Radford
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Stephanie L. Rayner
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Paulina Szwaja
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Marco Morsch
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Flora Cheng
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Tianyi Zhu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandQueenslandBrisbaneAustralia
| | - Jocelyn Widagdo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandQueenslandBrisbaneAustralia
| | - Victor Anggono
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandQueenslandBrisbaneAustralia
| | - Dean L. Pountney
- School of Pharmacy and Medical SciencesGriffith UniversityQueenslandGold CoastAustralia
| | - Roger Chung
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
| | - Albert Lee
- Centre for Motor Neuron Disease ResearchMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversityNew South WalesNorth RydeAustralia
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11
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Takashima JA, Woroniecka HA, Charest PG. Proximity Protein Labeling In Dictyostelium With Engineered Ascorbic Acid Peroxidase 2. J Biol Methods 2023; 10:e99010002. [PMID: 37007980 PMCID: PMC10062472 DOI: 10.14440/jbm.2023.396] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 03/18/2023] Open
Abstract
To fully understand any cellular process, we not only need to identify the proteins implicated, but also how the protein network is structurally and spatially organized and changes over time. However, the dynamic nature of many protein interactions involved in cellular signaling pathways continues to be the bottleneck in mapping and studying protein networks. Fortunately, a recently developed proximity labeling method using engineered ascorbic acid peroxidase 2 (APEX2) in mammalian cells allows the identification of weak and/or transient protein interactions with spatial and temporal resolution. Here, we describe a protocol for successfully using the APEX2-proximity labeling method in Dictyostelium, using the cAMP receptor cAR1 as example. Coupled to the identification of the labeled proteins by mass spectrometry, this method expands Dictyostelium's proteomics toolbox and should be widely useful for identifying interacting partners involved in a variety of biological processes in Dictyostelium.
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Affiliation(s)
- Jamie A. Takashima
- Department of Chemistry and Biochemistry, University of Arizona, Tucson AZ, USA
- Current address: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA, USA
| | | | - Pascale G. Charest
- Department of Chemistry and Biochemistry, University of Arizona, Tucson AZ, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson AZ, USA
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12
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Benstein RM, Schmid M, You Y. Isolation of Nuclei Tagged in Specific Cell Types (INTACT) in Arabidopsis. Methods Mol Biol 2023; 2686:313-328. [PMID: 37540367 DOI: 10.1007/978-1-0716-3299-4_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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Many functionally distinct plant tissues have relatively low numbers of cells that are embedded within complex tissues. For example, the shoot apical meristem (SAM) consists of a small population of pluripotent stem cells surrounded by developing leaves and/or flowers at the growing tip of the plant. It is technically challenging to collect enough high-quality SAM samples for molecular analyses. Isolation of Nuclei Tagged in specific Cell Types (INTACT) is an easily reproducible method that allows the enrichment of biotin-tagged cell-type-specific nuclei from the total nuclei pool using biotin-streptavidin affinity purification. Here, we provide a detailed INTACT protocol for isolating nuclei from the Arabidopsis SAM. One can also adapt this protocol to isolate nuclei from other tissues and cell types for investigating tissue/cell-type-specific transcriptome and epigenome and their changes during developmental programs at a high spatiotemporal resolution. Furthermore, due to its low cost and simple procedures, INTACT can be conducted in any standard molecular laboratory.
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Affiliation(s)
- Ruben M Benstein
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Markus Schmid
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yuan You
- Center for Plant Molecular Biology (ZMBP), Department of General Genetics, Eberhard Karls University of Tübingen, Tübingen, Germany.
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany.
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13
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Bhagwat SR, Choudhary K, Pandya N, Sharma S, Srivastava S, Kumar A, Hajela K. Identification of substrates of MBL Associated Serine Protease-1 (MASP-1) from human plasma using N-terminomics strategy. Mol Immunol 2022; 151:114-25. [PMID: 36126499 DOI: 10.1016/j.molimm.2022.09.001] [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] [Received: 04/13/2022] [Revised: 08/23/2022] [Accepted: 09/04/2022] [Indexed: 11/23/2022]
Abstract
MBL Associated Serine Protease-1 (MASP-1) is an abundant enzyme of the lectin complement pathway. MASP-1 cleaves numerous substrates like MASP-2, MASP-3, C2, C3i, fibrinogen, FXIII and prothrombin. It has thrombin-like specificity and can cleave thrombin substrates. Owing to its high concentration and relaxed substrate specificity, MASP-1 has substrates outside the complement system and can influence other proteolytic cascades and physiological processes. The unidentified substrates may assist us to ascertain the role(s) of MASP-1. In this study, we used a high-throughput N-terminomics method to identify substrates of MASP-1 from human plasma. We have identified 35 putative substrates of MASP-1. Among the identified proteins, alpha 2-antiplasmin, alpha-1-acid glycoprotein, antithrombin III, and siglec-6 were demonstrated to be cleaved by MASP-1. We have discussed the physiological relevance of cleavage of these substrates by MASP-1. The expression of Siglec-6 and MASP-1 has been reported in the B cells. Alpha-1-acid glycoprotein cleavage by MASP-1 may occur in the acute phase as it is known to be an inhibitor of platelet aggregation, whereas MASP-1 triggers platelet aggregation. The cleavage alpha2 antiplasmin by MASP-1 implies that MASP-1 may be promoting plasmin-mediated fibrinolysis. Our study supports that MASP-1 may be implicated in thrombosis as well as thrombolysis.
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14
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Yang J, Li X, Tong Y, Yang Y, Zhao L, Zhou Q, Xu J, Dong L, Jiang Y. Targeting co-delivery of doxorubicin and gefitinib by biotinylated Au NCs for overcoming multidrug resistance in imaging-guided anticancer therapy. Colloids Surf B Biointerfaces 2022; 217:112608. [PMID: 35679735 DOI: 10.1016/j.colsurfb.2022.112608] [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: 04/07/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
Abstract
Drug resistance and potential cardiotoxicity severely limit the DOX-mediated chemotherapy in clinical. Multi-drug combination is conducive to the realization of multi-modal synergy at the molecular level, which is crucial in drug dose optimization and improvement of therapeutic effect. In this work, fluorescent biotinylated Au Nanoclusters as an active targeting carrier was developed to realize real-time biological imaging and dual-drug delivery simultaneously. DNA toxin doxorubicin (DOX) and tyrosinase inhibitor gefitinib (GEF) were selected as dual-drug models for the treatment of human non-small cell lung cancer. The in vitro and in vivo results showed that dual-drug combination suppressed cancer cell growth more efficiently than any single formula at the same concentrations. GEF can block signaling in target cancer cells with mutated and overactive EGFR, thereby inhibiting tumor growth and metastasis and promoting tumor cell apoptosis. Combined with DOX chemotherapy, it will effectively overcome the problem of DOX resistance. In addition, the dual-drug delivery system produced excellent synergistic therapeutic effects without extra adverse toxicities. It provides a reference for the design and clinical application of the dual-drug delivery system.
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Affiliation(s)
- Jingjing Yang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, Shandong, China; Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
| | - Xiaofeng Li
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Yao Tong
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yufei Yang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Li Zhao
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Qian Zhou
- Key Laboratory of Birth Regulation and Control Technology of National Health and Family Planning Commission of China, Maternal Child Health Hospital of Shandong Province, Jinan, China
| | - Jiawen Xu
- Department of Pathology, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, Shandong 250021, China.
| | - Lun Dong
- Department of Breast Surgery, Qilu Hospital, Shandong University, Jinan, Shandong Province, China.
| | - Yanyan Jiang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, Shandong, China; Shenzhen Research Institute of Shandong University, Shenzhen 518057, China.
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15
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Siritutsoontorn S, Sukjoi W, Polyak SW, Akekawatchai C, Jitrapakdee S. Differential growth inhibition, cell cycle arrest and apoptosis of MCF-7 and MDA-MB-231 cells to holocarboxylase synthetase suppression. Biochem Biophys Res Commun 2022; 593:108-115. [PMID: 35063765 DOI: 10.1016/j.bbrc.2022.01.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/22/2021] [Accepted: 01/12/2022] [Indexed: 11/02/2022]
Abstract
Holocarboxylase synthetase (HLCS) catalyzes the covalent attachment of biotin onto the biotin-dependent carboxylases. Recent studies have shown that HLCS is over-expressed in breast cancer patients. Here we investigated the functional roles of free biotin and HLCS in supporting growth and migration of breast cancer cell lines. Depletion of biotin from culture medium markedly reduced biotinylation of the two most abundant biotin-carboxylases, acetyl-CoA carboxylase and pyruvate carboxylase. This was accompanied by a marked decrease in cell growth. Suppression of HLCS expression in the low invasive breast cancer cell line MCF-7 resulted in an 80% reduction of biotinylated ACC, but not PC. HLCS knockdown MCF-7 cell lines showed 40-50% reduction of proliferation and 35% reduction of migration, accompanied by G1 cell cycle-arrest-induced apoptosis. In contrast, knockdown of HLCS expression in the highly invasive cell line MDA-MB-231 resulted in only marginal reduction of biotinylation of both ACC and PC, accompanied by 30% reduction of proliferation and 30% reduction of migration. Our studies provide new insights to use HLCS as a novel anti-cancer drug target.
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Affiliation(s)
| | - Witchuda Sukjoi
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Steven W Polyak
- Clinical and Health Sciences, University of South Australia, Adelaide, Australia, 5001
| | - Chareeporn Akekawatchai
- Department of Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Sarawut Jitrapakdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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16
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Sharma P, Parveen S, Datta S. Measuring Plasma Membrane Recycling Using Microscopic and Biochemical Approaches. Methods Mol Biol 2022; 2473:237-257. [PMID: 35819770 DOI: 10.1007/978-1-0716-2209-4_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 endocytic pathway has an intricate network of vesicular compartments carrying a variety of proteins referred to as cargoes. Endosomal trafficking is exclusively required to transport these cargoes through various intracellular routes for their delivery to the site of action. Among these, recycling of cargoes to the plasma membrane is a crucial pathway for the efficient functioning of the cell. Hence, endosomal cargo recycling assays are crucial to gain insight into the molecular mechanism governing recycling of the cargoes and in turn to understand their key role in maintaining cellular physiology. These assays have been efficiently utilized to study the recycling of adhesion molecules, transporters, channels, receptors, and so on to the plasma membrane. The basic methodology involves labelling of the cargo at the surface, allowing its internalization followed by direct or indirect measurement of the amount of the cargo recycled back to the plasma membrane. These microscopy-based and biochemical methods can be used as a tool to study the role of various trafficking or signaling molecules on the cell surface involved with the recycling of the membrane proteins, by altering their expression either by silencing or overexpressing the gene.
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Affiliation(s)
- Priyanka Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
| | - Sameena Parveen
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Sunando Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
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17
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Abstract
Ascorbate peroxidase (APEX)-catalyzed proximity labeling has been recently established as a robust approach to uncover localized protein environments and transient protein-protein interactions occurring across mammalian cells. This molecular tool enables improved identification of individual proteins localized to and involved in specific cellular and subcellular pathways and functions. Engineering of an APEX2 fusion protein into the endogenous loci of proteins of interest enables directed biotinylation of neighboring polypeptides and mRNAs. This results in identification of subcellular and context-dependent proteomes or transcriptomes via quantitative mass spectrometry or RNA sequencing, respectively. Here, we describe the utility of APEX-mediated proximity labeling to recover components of stress granules (SGs) by endogenous tagging of well-established SG-associated proteins.
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Affiliation(s)
- Sara Elmsaouri
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sebastian Markmiller
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
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18
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Abstract
NOD-like receptors (NLRs) are established as key regulators of the innate immune system. In recent years, an increasing number of interaction partners have been described that modulate receptor activity by direct binding. Characterizing these interactions can be challenging because these receptors tend to adopt different conformational states. We have developed a protocol that employs intracellular protein biotinylation to provide a straightforward immobilization strategy in surface plasmon resonance experiments. With this highly sensitive and label-free technique, the kinetics and affinities of NLR and co-factor interactions can be measured directly at the protein level.
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Affiliation(s)
- Jonas Moecking
- Institute of Structural Biology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University Hospital Bonn, University of Bonn, Bonn, Germany.
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19
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Abstract
After isolation of a single-domain antibody (VHH) binding to an antigen of interest, the soluble VHH is often produced in Escherichia coli. However, targeting VHH expression to the secretory pathway of Saccharomyces cerevisiae (baker's yeast) enables the secretion of correctly folded, soluble, disulfide-bonded, and N-glycosylated VHHs into the culture medium. Here, we describe the small-scale production of VHHs in baker's yeast in shaker flasks using both an episomal vector and a vector requiring genomic integration for higher VHH expression levels. This expression system results in the production of VHHs linked to the natural llama long hinge region including a single cysteine residue for partial dimerization. This format is especially suitable for the development of double antibody sandwich ELISAs by passive adsorption of unlabeled VHHs to polystyrene ELISA plates, antigen capture, and detection of the antigen of interest using a second biotinylated VHH. The procedures described here for detection of foot-and-mouth disease virus can also be applied to other antigens for which suitable VHHs are available.
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20
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Reyes-Alvarez E, Walker TJ, Mulligan LM. Evaluating Cell Membrane Localization and Intracellular Transport of Proteins by Biotinylation. Methods Mol Biol 2022; 2508:197-209. [PMID: 35737242 DOI: 10.1007/978-1-0716-2376-3_15] [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
Protein translocation to the cell membrane and transport through intracellular compartments are dynamic processes frequently altered in cancer cells. Abnormal protein localization can affect key cell functions, including transduction of extracellular signals and organization of the cytoskeleton, significantly affecting oncogenicity and therapeutic responses. In this chapter, we describe a surface protein biotinylation method that allows the study of membrane localization and endosomal transport of membrane-associated proteins. Surface biotinylation can be used to evaluate baseline protein levels at the membrane, and other processes such as internalization, recycling, and degradation of proteins in response to different treatments or as a consequence of oncogenic mutations. Further, the combination of this technique with other strategies, such as treatments with transport inhibitors, allows investigation of specific steps of protein trafficking through the cell.
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Affiliation(s)
- Eduardo Reyes-Alvarez
- Division of Cancer Biology and Genetics, Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Timothy J Walker
- Division of Cancer Biology and Genetics, Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Lois M Mulligan
- Division of Cancer Biology and Genetics, Cancer Research Institute, Queen's University, Kingston, ON, Canada.
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21
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Abstract
We have utilized simple flow cytometric and fluorescence-based solid phase assays to study the interaction of glycan binding proteins (GBP) to cell surface glycoconjugates. These methods utilize commonly employed flow cytometry techniques and commercially available streptavidin-coated microplates to immobilize various biotinylated ligands, such as glycopeptides, oligosaccharides, and whole cells. Using this approach, fluorescently labeled GBPs, in particular, members of the galectin family, can be interrogated for potential interactions with cell surface carbohydrates, including elucidation of the potential impact of alterations in glycosylation on carbohydrate recognition. Using these approaches, we present examples of flow cytometric and fluorescence-based solid phase assays to study galectin-carbohydrate interactions.
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Affiliation(s)
| | - Connie M Arthur
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard Glycomics Center, Harvard Medical School, Boston, MA, USA
| | - Sean R Stowell
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard Glycomics Center, Harvard Medical School, Boston, MA, USA
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22
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Rajak MK, Sundd M. Chemical shift assignments of the biotin carboxyl carrier protein domain of L. major Methylcrotonyl-CoA carboxylase. Biomol NMR Assign 2021; 15:249-253. [PMID: 33751378 DOI: 10.1007/s12104-021-10013-y] [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] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
Methylcrotonyl-CoA carboxylase (MCCC) is a biotin dependent enzyme, that plays a crucial role in leucine metabolism. The enzyme comprises a biotin carboxylase (BC), a carboxyltransferase (CT), and a biotin carboxyl carrier protein (BCCP) domain. MCCC is synthesized as an apo-protein, and is posttranslationally modified at a lysine residue, conserved in the biotin carboxyl carrier protein (BCCP) domain. In order to understand the structure, function and interactions of L. major MCCC, we have expressed and characterized its domains. Here we report the complete chemical shift assignments of MCCC BCCP domain of L. major. Furthermore, we have used the assignments to generate a model of the same, using CS-Rosetta. We have also followed its chemical shift perturbations upon biotin modification. Changes were observed at the lysine 51 amide, that undergoes biotin modification, and a few others present in its immediate neighborhood.
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Affiliation(s)
- Manoj Kumar Rajak
- National Institute of Immunology, Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110 067, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110 067, India.
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23
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Ruan JL, Browning RJ, Yildiz YO, Bau L, Kamila S, Gray MD, Folkes L, Hampson A, McHale AP, Callan JF, Vojnovic B, Kiltie AE, Stride E. Evaluation of Loading Strategies to Improve Tumor Uptake of Gemcitabine in a Murine Orthotopic Bladder Cancer Model Using Ultrasound and Microbubbles. Ultrasound Med Biol 2021; 47:1596-1615. [PMID: 33707089 DOI: 10.1016/j.ultrasmedbio.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
In this study we compared three different microbubble-based approaches to the delivery of a widely used chemotherapy drug, gemcitabine: (i) co-administration of gemcitabine and microbubbles (Gem+MB); (ii) conjugates of microbubbles and gemcitabine-loaded liposomes (GemlipoMB); and (iii) microbubbles with gemcitabine directly bound to their surfaces (GembioMB). Both in vitro and in vivo investigations were carried out, respectively, in the RT112 bladder cancer cell line and in a murine orthotopic muscle-invasive bladder cancer model. The in vitro (in vivo) ultrasound exposure conditions were a 1 (1.1) MHz centre frequency, 0.07 (1.0) MPa peak negative pressure, 3000 (20,000) cycles and 100 (0.5) Hz pulse repetition frequency. Ultrasound exposure produced no significant increase in drug uptake either in vitro or in vivo compared with the drug-only control for co-administered gemcitabine and microbubbles. In vivo, GemlipoMB prolonged the plasma circulation time of gemcitabine, but only GembioMB produced a statistically significant increase in cleaved caspase 3 expression in the tumor, indicative of gemcitabine-induced apoptosis.
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Affiliation(s)
- Jia-Ling Ruan
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Richard J Browning
- Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Yesna O Yildiz
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Luca Bau
- Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Sukanta Kamila
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, United Kingdom
| | - Michael D Gray
- Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Lisa Folkes
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Alix Hampson
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Anthony P McHale
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, United Kingdom
| | - John F Callan
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, United Kingdom
| | - Borivoj Vojnovic
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Anne E Kiltie
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Eleanor Stride
- Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom.
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24
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Abstract
Cellular compartmentalization of proteins and protein complex formation allow cells to tightly control biological processes. Therefore, understanding the subcellular localization and interactions of a specific protein is crucial to uncover its biological function. The advent of proximity labeling (PL) has reshaped cellular proteomics in infection biology. PL utilizes a genetically modified enzyme that generates a "labeling cloud" by covalently labeling proteins in close proximity to the enzyme. Fusion of a PL enzyme to a specific antibody or a "bait" protein of interest in combination with affinity enrichment mass spectrometry (AE-MS) enables the isolation and identification of the cellular proximity proteome, or proxisome. This powerful methodology has been paramount for the mapping of membrane or membraneless organelles as well as for the understanding of hard-to-purify protein complexes, such as those of transmembrane proteins. Unsurprisingly, more and more infection biology research groups have recognized the potential of PL for the identification of host-pathogen interactions. In this chapter, we introduce the enzymes commonly used for PL labeling as well as recent promising advancements and summarize the major achievements in organelle mapping and nucleic acid PL. Moreover, we comprehensively describe the research on host-pathogen interactions using PL, giving special attention to studies in the field of virology.
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Affiliation(s)
- Francisco José Zapatero-Belinchón
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
| | - Belén Carriquí-Madroñal
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Gisa Gerold
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
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25
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Wiseman E, Bates L, Carroll DJ. Recovery of Sea Star Egg Cell Surface Proteins Released at Fertilization. Methods Mol Biol 2021; 2219:151-61. [PMID: 33074539 DOI: 10.1007/978-1-0716-0974-3_9] [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
To provide a better understanding of the composition of the egg cell membrane, we describe a method in which proteins and peptides that are either naturally released by the egg or cleaved by sperm proteases can be collected, analyzed, and identified. Such molecules are captured and isolated from the surrounding seawater via biotinylation, before being concentrated by an affinity interaction and subsequently analyzed by western blotting and mass spectrometry.
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26
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Taher Z, Legge C, Winder N, Lysyganicz P, Rawlings A, Bryant H, Muthana M, Staniland S. Magnetosomes and Magnetosome Mimics: Preparation, Cancer Cell Uptake and Functionalization for Future Cancer Therapies. Pharmaceutics 2021; 13:367. [PMID: 33802121 PMCID: PMC7998144 DOI: 10.3390/pharmaceutics13030367] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/17/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 11/16/2022] Open
Abstract
Magnetic magnetite nanoparticles (MNP) are heralded as model vehicles for nanomedicine, particularly cancer therapeutics. However, there are many methods of synthesizing different sized and coated MNP, which may affect their performance as nanomedicines. Magnetosomes are naturally occurring, lipid-coated MNP that exhibit exceptional hyperthermic heating, but their properties, cancer cell uptake and toxicity have yet to be compared to other MNP. Magnetosomes can be mimicked by coating MNP in either amphiphilic oleic acid or silica. In this study, magnetosomes are directly compared to control MNP, biomimetic oleic acid and silica coated MNP of varying sizes. MNP are characterized and compared with respect to size, magnetism, and surface properties. Small (8 ± 1.6 nm) and larger (32 ± 9.9 nm) MNP are produced by two different methods and coated with either silica or oleic acid, increasing the size and the size dispersity of the MNP. The coated larger MNP are comparable in size (49 ± 12.5 nm and 61 ± 18.2 nm) to magnetosomes (46 ± 11.8 nm) making good magnetosome mimics. All MNP are assessed and compared for cancer cell uptake in MDA-MB-231 cells and importantly, all are readily taken up with minimal toxic effect. Silica coated MNP show the most uptake with greater than 60% cell uptake at the highest concentration, and magnetosomes showing the least with less than 40% at the highest concentration, while size does not have a significant effect on uptake. Finally, surface functionalization is demonstrated for magnetosomes and silica coated MNP using biotinylation and EDC-NHS, respectively, to conjugate fluorescent probes. The modified particles are visualized in MDA-MB-231 cells and demonstrate how both naturally biosynthesized magnetosomes and biomimetic silica coated MNP can be functionalized and readily up taken by cancer cells for realization as nanomedical vehicles.
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Affiliation(s)
- Zainab Taher
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK; (Z.T.); (C.L.); (N.W.); (P.L.); (A.R.)
| | - Christopher Legge
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK; (Z.T.); (C.L.); (N.W.); (P.L.); (A.R.)
- Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK; (H.B.); (M.M.)
| | - Natalie Winder
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK; (Z.T.); (C.L.); (N.W.); (P.L.); (A.R.)
- Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK; (H.B.); (M.M.)
| | - Pawel Lysyganicz
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK; (Z.T.); (C.L.); (N.W.); (P.L.); (A.R.)
- Department of Biomedical Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Andrea Rawlings
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK; (Z.T.); (C.L.); (N.W.); (P.L.); (A.R.)
| | - Helen Bryant
- Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK; (H.B.); (M.M.)
| | - Munitta Muthana
- Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK; (H.B.); (M.M.)
| | - Sarah Staniland
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, UK; (Z.T.); (C.L.); (N.W.); (P.L.); (A.R.)
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27
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Abstract
Proteome networks are a crucial facet of biological systems that mediate cellular functions and responses to the environment. However, a main limitation of traditional approaches to study protein interactions, such as yeast-2-hybrid and affinity purification-coupled with mass spectrometry (AP-MS), is their restricted ability to identify interactions for membrane-bound and/or insoluble protein complexes. These types of interactions include many of the protein complexes that mediate the perception and response to cellular stimuli and are therefore of great research interest. Proximity-dependent biotinylation (PDB) coupled to mass spectrometry provides a powerful approach to survey proximal protein interactions in living cells, including membrane bound and insoluble complexes. One PDB method, BioID, translationally fuses a promiscuous biotin ligase to a bait protein of interest, allowing covalent biotinylation of proximal proteins (within ~10 nm). Modified proteins can be purified from cells without the need to maintain protein interactions, and subsequently identified by mass spectrometry. Although BioID has revolutionized the study of proteomes in numerous organisms, its application to plant systems has only recently been realized. In this chapter, we outline a protocol for BioID in tissues of the model plant Arabidopsis thaliana.
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Affiliation(s)
- Madiha Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Darrell Desveaux
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.
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28
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Abstract
Biotinylation identification (BioID) is a method designed to provide new cellular location and functional knowledge of the protein of interest through the identification of those proteins surrounding and in direct contact. A biotin ligase is fused onto the protein of interest and expressed in cells where it can biotinylate even short-lived transient protein complexes. In addition, due to the proximity labeling nature of the experiment, cellular localization and functional enrichment information can also be obtained. Since labeling occurs only after the addition of biotin, temporal relationships and localization changes (e.g., cytoplasmic to nuclear) can also be identified. Labeled proteins are easily purified, and contaminants minimized, using the strong interaction between biotin and streptavidin. Mass spectrometry analysis of the purified proteins allows for the identification of potential interactors for further validation and characterization.
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Taniyama T, Sueda S. Fluorescent Labeling of the Nuclear Envelope Without Relying on Inner Nuclear Membrane Proteins. Methods Mol Biol 2021; 2274:3-14. [PMID: 34050457 DOI: 10.1007/978-1-0716-1258-3_1] [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: 12/28/2022]
Abstract
The nuclear envelope (NE), a double membrane that separates nuclear components from the cytoplasm, undergoes a breakdown and reformation during cell division. To trace NE dynamics, the NE needs to be labeled with a fluorescent marker, and for this purpose, markers based on inner nuclear membrane (INM) proteins are normally used. However, NE labeling with INM proteins has some limitations. Here, we introduce a protocol for fluorescent labeling and imaging of NE that does not rely on INM proteins, along with protocols for simultaneously imaging two nuclear components and for time-lapse imaging of labeled cells.
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Santos T, Hébraud M. Extraction and Preparation of Listeria monocytogenes Subproteomes for Mass Spectrometry Analysis. Methods Mol Biol 2021; 2220:137-53. [PMID: 32975772 DOI: 10.1007/978-1-0716-0982-8_11] [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
Proteomics has become an essential tool to answer biologists' questions. For bacteriologists, the proteome of bacteria is much less complex than that of eukaryotic organisms. However, not all the different cell "compartments" are easily accessible, and the analysis of cell envelope proteins is particularly challenging. For the Gram-positive bacterium Listeria monocytogenes, one of the main foodborne pathogen microorganisms, the study of surface proteins is crucial to better understand the mechanisms of pathogenicity, as well as adaptation/resistance to and persistence in hostile environments. The evolution of proteomic techniques, and particularly the possibility of separating and analyzing complex protein samples by off-gel (LC-MS/MS) versus in-gel (two-dimensional electrophoresis) approach, has opened the doors to new extraction and preparation methods to target the different subproteomes. Here, we describe three procedures to prepare and analyze intracellular, exocellular, and cell surface proteins: (1) the cell fractionation, based on cell broken and separation of protein subfractions by differential centrifugation; (2) the biotinylation, based on the labeling of cell surface proteins and their selective extraction; and (3) the enzymatic shaving by the action of trypsin on intact cells. These complementary methods allow to encompass all L. monocytogenes subproteomes for general profiling or target studies and could be applicable to other Gram-positive bacteria.
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Jin X, Cao X, Liu B. Isolation of Aged Yeast Cells Using Biotin-Streptavidin Affinity Purification. Methods Mol Biol 2021; 2196:223-8. [PMID: 32889724 DOI: 10.1007/978-1-0716-0868-5_17] [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
Yeast (Saccharomyces cerevisiae) has been used as one of the main model systems for studying molecular mechanisms underlying cellular aging. A major technical challenge in studying aging in yeast is the isolation of aged cells from exponentially growing cell cultures, since aged cells in such cultures are rare. Several methods for isolating aged cells have been developed to achieve this. Here, we describe a biotin-streptavidin affinity purification protocol for isolating aged yeast cells. It consists of three main steps: biotinylation of yeast cells, culturing cells to the desired age, and harvesting the aged cells using streptavidin-coated magnetic microbeads. The isolated aged cells can be used for microscopy, biochemistry, or molecular biology analysis.
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Anand RS, Ganesan D, Selvam S, Rajasekaran S, Jayavelu T. Distinct utilization of biotin in and between adipose and brain during aging is associated with a lipogenic shift in Wistar rat brain. Nutr Res 2020; 79:68-76. [PMID: 32650222 DOI: 10.1016/j.nutres.2020.06.004] [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: 02/21/2020] [Revised: 05/12/2020] [Accepted: 06/02/2020] [Indexed: 11/25/2022]
Abstract
Tissue-specific metabolism determines their functions that collectively sense and respond to numerous stress cues to achieve systemic homeostasis. Chronic stress skews such metabolic profiles and leads to failure of organs as evidenced by a bias towards lipid synthesis and storage in the aging brain, muscle, and liver under Alzheimer's disease, sarcopenia, and non-alcoholic fatty liver disease, respectively. In contrast, the tissue destined for lipid synthesis and storage, such as adipose, limits its threshold and develops diabetes mellitus. However, the underlying factors that contribute to this lipogenic shift between organs are unknown. From this perspective, differential biotin utilization between lipid-rich tissues such as adipose and brain during aging was hypothesized owing to the established role of biotin in lipogenesis. The same was tested using young and aged Wistar rats. We found that adipose-specific biotin content was much higher than the brain irrespective of aging status, as well as its associated cues. However, within tissues, the adipose fails to maintain its biotinylation levels during aging whereas the brain seizes more biotin and exhibits lipid accumulation. Furthermore, mimicking the age-related stress cues in vitro such as high glucose and endoplasmic reticulum stress deprive the astroglial biotin content, but not that of adipocytes. Lipid accumulation in the aging brain was also correlated with increased S-adenosylmethionine levels and biotin utilization by astrocytes. In summary, differential biotin utilization between adipose and brain under aging and their respective cell types like adipocytes and astrocytes under age-associated stress cues connects well with the lipogenic shift in rat brain.
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Huang L, Bao H, Li S, Zhang J, Li L, Zhang B, Yu Y, Liu Y, Li H. Improvement of the sensitivity of the detection of Gal d 6-specific IgE via biotinylation in vivo. Allergol Immunopathol (Madr) 2020; 48:348-54. [PMID: 32532469 DOI: 10.1016/j.aller.2020.02.002] [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] [Received: 09/29/2019] [Revised: 01/22/2020] [Accepted: 02/06/2020] [Indexed: 11/23/2022]
Abstract
INTRODUCTION AND OBJECTIVES This study aimed to compare the effects of different biotinylation methods on the performance characteristics of allergen-specific IgE detection. MATERIALS AND METHODS The Gal d 6 gene was cloned into the pAN6/pAC6 vector, resulting in rGal d 6-Bio/Bio-rGal d 6 vector. The fusion protein was expressed in Escherichia coli AVB101 and simultaneously biotinylated in a site-specific manner. The Gal d 6 gene was amplified via PCR and cloned into the pET-28a vector and transformed into E. coli BL21 and purified via Ni-NTA, followed by chemical biotinylation using Sulfo-NHS-LC-Biotin. Twenty-eight patients allergic to hen's egg white were examined for sensitization against egg yolk. An antigen-capture enzyme-linked immunosorbent assay (AC-ELISA) was developed to detect allergen-specific IgE. RESULTS rGal d 6, Bio-rGal d 6, and rGal d 6 were prepared using different biotin binding modes to detect allergen-specific IgE. rGal d 6-Bio (Kd=0.6154) and Bio-rGal d 6 (Kd=0.6698) had a markedly better detection performance than rGal d 6 (Kd=28.93), and the rGal d 6-Bio had a better detection performance in small-volume serum samples. CONCLUSIONS rGal d 6-Bio improved the sensitivity for the detection of allergen-specific IgE.
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Shinya T, Shibuya N, Kaku H. Affinity Labeling and Purification of Plant Chitin-Binding LysM Receptor with Chitin Octasaccharide Derivatives. Methods Mol Biol 2020; 2132:401-412. [PMID: 32306347 DOI: 10.1007/978-1-0716-0430-4_39] [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
Lysin motif (LysM) is a carbohydrate-binding modules found in all kingdoms. LysM binds to N-acetylglucosamine-containing molecules such as peptidoglycan, chitin, Nod factor, and Myc factor and is found in peptidoglycan hydrolases, chitinases, and plant pathogen effectors and plant receptor/co-receptor for defense and symbiosis signaling. This chapter describes the synthesis of a nonradioactive chitin ligand, biotinylated chitin octasaccharide, (GlcNAc)8-Bio, and its application for the detection and characterization of chitin-binding LysM receptor CEBiP in the microsomal membrane fraction of rice suspension-cultured cells by affinity labeling. We also describe the purification of CEBiP from the plasma membrane of the rice cells by affinity chromatography with the synthesized (GlcNAc)8-APEA-CH-Sepharose as an affinity matrix.
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Affiliation(s)
- Tomonori Shinya
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Hanae Kaku
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan.
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Abstract
Most, if not all, plasma membrane proteins continuously undergo endocytosis and many rapidly recycle from endosomes back to the cell surface to maintain "stable" surface expression. We now describe a biochemical assay that is suited to follow the internalization and recycling kinetics of plasma membrane proteins. This assay involves biotinylation of plasma membrane proteins using sulfo-NHS-SS-biotin, a water-soluble, NHS-ester biotinylation reagent that contains a cleavable disulfide bond that allows for reversible labeling of proteins. Biotinylation is rapid and stable, and does not transfer from cell to cell, and the small size of the biotin probe does not affect cell function.
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Mukherjee J, Franz-Wachtel M, Maček B, Jansen RP. RNA Interactome Identification via RNA-BioID in Mouse Embryonic Fibroblasts. Bio Protoc 2020; 10:e3476. [PMID: 33654709 DOI: 10.21769/bioprotoc.3476] [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: 07/27/2019] [Revised: 11/20/2019] [Accepted: 12/28/2019] [Indexed: 11/02/2022] Open
Abstract
Cytoplasmic localization of mRNAs is common to all organisms and serves the spatial expression of genes. Cis-acting RNA signals (mostly found in the mRNA's 3'-UTR), called zipcodes recruit trans-acting RNA-binding proteins that facilitate the localization of the mRNA. UV-cross-linking or affinity purification has been applied to identify such proteins but suffer from the need for stable RNA-protein binding or direct contact of protein and RNA. To identify stably or transiently interacting proteins that directly or indirectly associated with the localization elements and the body of the mRNA, we developed an in vivo proximity labeling method we call RNA-BioID. In RNA-BioID, we tether a fusion of the BirA* biotin ligase and the MS2 coat protein (MCP) at the 3'-UTR of MS2-tagged β-actin mRNA in vivo. Exposing BirA* expressing cells to biotin in the media and induces biotinylation of β-actin mRNA-associated proteins that can be isolated with streptavidin beads. This technique allowed us to identify by mass spectrometry analysis the β-actin mRNA 3'-UTR-interacting proteome in fibroblasts. The protocol can be useful to identify the interacting proteome of any mRNA in mammalian cells.
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Affiliation(s)
- Joyita Mukherjee
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | | | - Boris Maček
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Ralf-Peter Jansen
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
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Abstract
Streptococcus pyogenes utilizes extracellular cellular matrix (ECM) proteins to adhere to human tissues and internalize into host cells. Fibronectin (Fn) is one of the most abundant ECM proteins and targeted by a wide variety of secreted Fn-binding proteins (Fbps) of S. pyogenes. However, prior to detailed kinetic analysis of that binding process, evaluations of the ability of S. pyogenes strains to bind to Fn as well as interactions of target molecules with Fn are required. In this chapter, we present routine procedures for ligand blot analysis with labeled human Fn, using bacterial cell wall extracts prepared by either enzymatic digestion of cells or extraction with a denaturing agent.
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Affiliation(s)
- Masanobu Nakata
- Department of Oral and Molecular Microbiology, Graduate School of Dentistry, Osaka University, Suita-Osaka, Japan
| | - Shigetada Kawabata
- Department of Oral and Molecular Microbiology, Graduate School of Dentistry, Osaka University, Suita-Osaka, Japan.
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Wei C. Assessing ADC Plasma Stability by LC-MS Methods. Methods Mol Biol 2020; 2078:353-359. [PMID: 31643070 DOI: 10.1007/978-1-4939-9929-3_25] [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: 06/10/2023]
Abstract
Plasma stability of ADCs can have a profound impact on ADC efficacy and safety. LC-MS methods enable the detection and characterization of ADC to evaluate its stability in plasma. Here we describe a procedure and LC-MS method for assessing ADC plasma stability.
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Affiliation(s)
- Cong Wei
- Drug Metabolism and Pharmacokinetics, Biogen Inc., Cambridge, MA, USA.
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Santamaria S. Chemical Modification of Proteoglycanases with Biotin. Methods Mol Biol 2020; 2043:113-123. [PMID: 31463907 DOI: 10.1007/978-1-4939-9698-8_10] [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: 06/10/2023]
Abstract
Biotinylation is a versatile technique that has been used to label proteins for a variety of applications. Under alkaline conditions, the N-hydroxylsuccinimide (NHS) ester present on the biotinylation reagent reacts with primary amines such as the side chain of lysine residues or the N-termini of proteins to yield stable amide bonds. However, the effect of biotinylation on enzyme structure and function has not been generally appreciated. In this chapter, I describe specific issues involving biotinylation of proteoglycanases (e.g., ADAMTS-1, -4, and -5). Taking ADAMTS-5 as an example, I show how high incorporation of biotin molecules causes a decrease in aggrecanase activity, most likely by disrupting exosites present in the cysteine-rich and spacer domains. Such an effect is not evident when enzymatic activity is measured with synthetic peptides, since exosites are not strictly required for peptidolytic activity. Therefore, extreme care must be taken when labeling proteoglycanases and the appropriate enzyme/biotin ratio must be determined experimentally for each enzyme.
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Liang Z, Li P, Wang C, Singh D, Zhang X. Visualizing the Transport of Porcine Reproductive and Respiratory Syndrome Virus in Live Cells by Quantum Dots-Based Single Virus Tracking. Virol Sin 2019; 35:407-416. [PMID: 31872331 DOI: 10.1007/s12250-019-00187-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 08/20/2019] [Accepted: 10/09/2019] [Indexed: 01/10/2023] Open
Abstract
Quantum dots (QDs)-based single particle analysis technique enables real-time tracking of the viral infection in live cells with great sensitivity over a long period of time. The porcine reproductive and respiratory syndrome virus (PRRSV) is a small virus with the virion size of 40-60 nm which causes great economic losses to the swine industry worldwide. A clear understanding of the viral infection mechanism is essential for the development of effective antiviral strategies. In this study, we labeled the PRRSV with QDs using the streptavidin-biotin labeling system and monitored the viral infection process in live cells. Our results indicated that the labeling method had negligible effect on viral infectivity. We also observed that prior to the entry, PRRSV vibrated on the plasma membrane, and entered the cells via endosome mediated cell entry pathway. Viruses moved in a slow-fast-slow oscillatory movement pattern and finally accumulated in a perinuclear region of the cell. Our results also showed that once inside the cell, PRRSV moved along the microtubule, microfilament and vimentin cytoskeletal elements. During the transport process, virus particles also made contacts with non-muscle myosin heavy chain II-A (NMHC II-A), visualized as small spheres in cytoplasm. This study can facilitate the application of QDs in virus infection imaging, especially the smaller-sized viruses and provide some novel and important insights into PRRSV infection mechanism.
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Affiliation(s)
- Zhenpu Liang
- College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), Henan Agricultural University, Zhengzhou, 450000, China
| | - Pengjuan Li
- College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), Henan Agricultural University, Zhengzhou, 450000, China
| | - Caiping Wang
- College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), Henan Agricultural University, Zhengzhou, 450000, China
| | - Deepali Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, 201312, India
| | - Xiaoxia Zhang
- College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology (Ministry of Agriculture), Henan Agricultural University, Zhengzhou, 450000, China.
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Bhagwat SR, Hajela K, Bhutada S, Choudhary K, Saxena M, Sharma S, Kumar A. Identification of unexplored substrates of the serine protease, thrombin, using N-terminomics strategy. Int J Biol Macromol 2020; 144:449-59. [PMID: 31862363 DOI: 10.1016/j.ijbiomac.2019.12.137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/15/2019] [Accepted: 12/15/2019] [Indexed: 12/13/2022]
Abstract
The function and regulation of thrombin is a complex as well as an intriguing aspect of evolution and has captured the interest of many investigators over the years. The reported substrates of thrombin are coagulation factors V, VIII, XI, XIII, protein C and fibrinogen. However, these may not be all the substrate of thrombin and therefore its functional role(s), may not have been completely comprehended. The purpose of our study was to identify hitherto unreported substrates of thrombin from human plasma using a N-terminomics protease substrate identification method. We identified 54 putative substrates of thrombin of which 12 are already known and 42 are being reported for the first time. Amongst the proteins identified, recombinant siglec-6 and purified serum alpha-1-acid glycoprotein were validated by cleavage with thrombin. We have discussed the probable relevance of siglec-6 cleavage by thrombin in human placenta mostly because an upregulation in the expression of siglec-6 and thrombin has been reported in the placenta of preeclampsia patients. We also speculate the role of alpha-1-acid glycoprotein cleavage by thrombin in the acute phase as alpha-1-acid glycoprotein is known to be an inhibitor of platelet aggregation whereas thrombin is known to trigger platelet aggregation.
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Dwivedi-Agnihotri H, Srivastava A, Shukla AK. Reversible biotinylation of purified proteins for measuring protein-protein interactions. Methods Enzymol 2019; 633:281-294. [PMID: 32046851 DOI: 10.1016/bs.mie.2019.11.008] [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: 12/28/2022]
Abstract
Measuring protein-protein interactions using purified proteins in vitro is one of the most frequently used approach to understand the biochemical and mechanistic details of cellular signaling pathways. Typically, affinity tags are genetically fused to proteins of interest, and they are used to capture and detect them. However, in some cases, fusion of bulky affinity tags might present a significant limitation in these experiments, especially if the regions in close proximity of tags are involved in protein-protein interactions. Here, we present a step-by-step protocol for an alternative approach that involves reversible biotinylation of purified proteins using a simple chemical-conjugation of cleavable biotin moiety. Biotinylated proteins can be directly used as bait for selective immobilization on solid support for measuring protein-protein interactions. Furthermore, biotinylation of protein of interest also allows specific detection in standard biochemical assays. This simple, straightforward and modular protocol can be directly adapted and applied to facilitate the detection of novel protein-protein interactions as well as measuring apparent affinities of such interactions.
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Affiliation(s)
| | - Ashish Srivastava
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India.
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De Rosa L, Di Stasi R, Longhitano L, D'Andrea LD. Labeling of VEGFR1D2 through oxime ligation. Bioorg Chem 2019; 91:103160. [PMID: 31398600 DOI: 10.1016/j.bioorg.2019.103160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 06/19/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 02/06/2023]
Abstract
We reported an useful protocol for the labeling of the second domain of the Vascular Endothelial Growth Factor Receptor 1 (VEGFR1D2), a small protein ligand able to bind VEGF, the main regulator of angiogenesis. We developed a bioconjugation strategy based on the use of oxime-ligation reaction conjugating an aldehyde derivative of the VEGFR1D2 to a molecular probe harboring an alkoxyamine functional group. We applied the synthetic protocol to prepare a biotinylated conjugate of VEGFR1D2 and we demonstrate that the bioconjugate retains its ability to specifically bind its natural ligand, VEGF, with high affinity. The biotinylated VEGFR1D2 could be useful to detect and quantify VEGF for diagnostic purposes as well as a tool for the screening of new molecules targeting VEGFRs for therapeutic applications. The labeling protocol is versatile and can be extended to different molecular probes, such as fluorophores, chelators or multimeric scaffolds, affording a biomedical platform for VEGF targeting.
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Affiliation(s)
- Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Rossella Di Stasi
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Laura Longhitano
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Luca Domenico D'Andrea
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80134 Napoli, Italy; Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Nizza 52, 10126 Torino, Italy.
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Abstract
Proximity-dependent labeling methods for detecting candidate protein-protein interactions (PPIs) or mapping the protein constituency of subcellular domains have become increasingly utilized by the scientific community. One such method, BioID, allows for the identification of not only strong interactions but also weak and transient associations between a protein of interest (POI) or targeting motif and adjacent proteins. A promiscuous biotin ligase is fused to a POI or targeting motif, expressed in living cells, and induced to biotinylate proximal proteins during a defined labeling period by biotin supplementation. This generates a history of protein-protein associations that occurred with the POI or the protein constituency within a discrete subcellular domain during the labeling period. Biotinylated proteins are subsequently isolated, identified via mass spectrometry, and investigated as candidate interactors with the POI or as constituents within a subcellular domain. The BioID method has been utilized by numerous research groups and is continually being optimized, applied to new models, and modified for use in novel applications. Here we describe a protocol by which a BioID fusion protein can be validated and utilized for BioID pull-downs.
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Affiliation(s)
- Danielle G May
- Enabling Technology Group, Sanford Research, Sioux Falls, SD, USA
| | - Kyle J Roux
- Enabling Technology Group, Sanford Research, Sioux Falls, SD, USA.
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA.
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Samal S, Bansal M, Das S. Method to identify efficiently cleaved, membrane-bound, functional HIV-1 (Human Immunodeficiency Virus-1) envelopes. MethodsX 2019; 6:837-849. [PMID: 31049300 PMCID: PMC6484210 DOI: 10.1016/j.mex.2019.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 07/24/2018] [Accepted: 04/09/2019] [Indexed: 10/29/2022] Open
Abstract
An ideal vaccine against HIV-1 will specifically elicit bNAbs (broadly neutralizing antibodies) which can cross-neutralize a wide spectrum of circulating viral strains belonging to different clades. The current paradigm for developing such a vaccine is to generate HIV-1 envelope (Env)-based immunogens which can specifically elicit bNAbs. For this purpose, it is necessary to identify Envs, belonging to different clades, suitable for immunogen design. Efficient cleavage of the HIV-1 Env precursor gp160 polypeptide into its constituent subunits determines its ability to selectively bind to bNAbs and poorly to non-NAbs (non-neutralizing antibodies), properties desirable in Env-based immunogens. Thus, efficiently cleaved HIV-1 Envs with desirable antigenic properties can be good candidates for developing immunogens. Here we describe in detail a six step method we have used in our laboratory to identify such efficiently cleaved Envs. Some of these protocols are optimizations of previously reported assays such as FACS-based cell surface antibody binding assay, pseudovirus neutralization assay and gp120 shedding assay. Other protocols like biotinylation-neutravidin-agarose pull-down assay and plasma membrane protein immunoprecipitation assay have been developed by taking inputs from reagent/kit manufacturer's protocols and previous studies. These protocols will help the field in identifying more such Envs which can be used for immunogen development. •Six step process to identify efficiently cleaved, membrane-bound, functional HIV-1 Envs with high degree of repeatability.•Method applicable for characterizing any HIV-1 envelope protein.•New method of immunoprecipitation of plasma membrane fraction to validate efficiently cleaved HIV-1 envelopes.
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Affiliation(s)
- Sweety Samal
- THSTI-IAVI HIV Vaccine Design Program, Translational Health Science and Technology Institute, Faridabad, 121001, Haryana, India
| | - Manish Bansal
- THSTI-IAVI HIV Vaccine Design Program, Translational Health Science and Technology Institute, Faridabad, 121001, Haryana, India
| | - Supratik Das
- THSTI-IAVI HIV Vaccine Design Program, Translational Health Science and Technology Institute, Faridabad, 121001, Haryana, India
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Abstract
The isolation of antibody fragments targeting proteins implicated in cancers and other diseases remains a crucial issue on targeted therapy or diagnostic tool development. In many case, the protein of interest, or a relevant portion of this protein such as its extracellular domain, is available as purified protein. In such cases, phage display on purified antigen is an easy and fast way to select antibody fragment able to efficiently bind this antigen. However the output of phage selection can vary significantly depending on the way to immobilize the purified antigen during selection. The following protocols describe the selection of phage antibody on purified antigen adsorbed on plastic, i.e., panning, or a selection in solution, using a biotinylated antigen as well as the corresponding screening produces, and give hints on the advantage and drawbacks of each approach.
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Affiliation(s)
- Magali Colazet
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Institut Paoli-Calmettes, Aix Marseille University, Marseille, France
| | - Patrick Chames
- Institut Paoli-Calmettes, CRCM, Aix Marseille University, CNRS, INSERM, Marseille, France.
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Li Y, Wang Y, Mao J, Yao Y, Wang K, Qiao Q, Fang Z, Ye M. Sensitive profiling of cell surface proteome by using an optimized biotinylation method. J Proteomics 2019; 196:33-41. [PMID: 30707948 DOI: 10.1016/j.jprot.2019.01.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 01/23/2023]
Abstract
Cell surface proteins are responsible for many critical functions. Systematical profiling of these proteins would provide a unique molecular fingerprint to classify cells and provide important information to guide immunotherapy. Cell surface biotinylation method is one of the effective methods for cell surface proteome profiling. However, classical workflows suffer the disadvantage of poor sensitivity. In this work, we presented an optimized protocol which enabled identification of more cell surface proteins from a smaller number of cells. When this protocol was combined with a tip based fractionation scheme, 4510 proteins, including 2055 annotated cell surface-associated proteins, were identified with only 20 microgram protein digest, showing the superior sensitivity of the approach. To enable process 10 times fewer cells, a pipet tip based protocol was developed, which led to the identification of about 600 cell surface-associated proteins. Finally, the new protocol was applied to compare the cell surface proteomes of two breast cancer cell lines, BT474 and MCF7. It was found that many cell surface-associated proteins were differentially expressed. The new protocols were demonstrated to be easy to perform, time-saving, and yielding good selectivity and high sensitivity. We expect this protocol would have broad applications in the future. SIGNIFICANCE: Cell surface proteins confer specific cellular functions and are easily accessible. They are often used as drug targets and potential biomarkers for prognostic or diagnostic purposes. Thus, efficient methods for profiling cell surface proteins are highly demanded. Cell surface biotinylation method is one of the effective methods for cell surface proteome profiling. However, classical workflows suffer the disadvantage of poor sensitivity. In this work, we presented an optimized protocol which enabled identification of more cell surface proteins from a smaller number of starting cells. The new protocol is easier to perform, time-saving and has less protein loss. By using a special pipet tip, sensitive and in-depth cell surface proteome analysis could be achieved. In combination with label-free quantitative MS, the new protocol can be applied to the differential analysis of the cell surface proteomes between different cell lines to find genetically- or drug-induced changes. We expect this protocol would have broad application in cell surface protein studies, including the discovery of diagnostic marker proteins and potential therapeutic targets.
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Abstract
Lipid droplets (LDs) are ubiquitous lipid storage organelles composed of a neutral lipid core surrounded by a phospholipid monolayer that is decorated with integral and peripheral proteins. Accurate identification of LD proteins using biochemical fractionation methods has been challenging due to the presence of contaminant proteins from co-fractionating organelles. Here, we describe a method to identify high-confidence LD proteomes that employs an engineered ascorbate peroxidase (APEX2) to induce spatially and temporally restricted biotinylation of LD proteins. This proximity labeling method can be broadly applied to define the composition of the LD proteome in any cultured cell line and can be utilized to examine LD proteome dynamics.
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Abstract
BioID has become an increasingly utilized tool for identifying candidate protein-protein interactions (PPIs) in living cells. This method utilizes a promiscuous biotin ligase, called BioID, fused to a protein of interest that when expressed in cells can be induced to biotinylate interacting and proximate proteins over a period of hours, thus generating a history of protein associations. These biotinylated proteins are subsequently purified and identified via mass spectrometry. Compared to other conventional methods typically used to screen strong PPIs, BioID allows for the detection of weak and transient interactions within a relevant biological setting over a defined period of time. Here we briefly review the scientific progress enabled by the BioID technology, detail an updated protocol for applying the method to proteins in living cells, and offer insights for troubleshooting commonly encountered setbacks.
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Affiliation(s)
- Rhiannon M. Sears
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104,Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD 57069
| | - Danielle G. May
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104
| | - Kyle J. Roux
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104,Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105
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Rice GM, Nutiu R, Gampe CM. Direct Chemical Biotinylation of RNA 5'-Ends Using a Diazo Reagent. Methods Mol Biol 2018; 1870:81-87. [PMID: 30539548 DOI: 10.1007/978-1-4939-8808-2_6] [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: 03/05/2023]
Abstract
Introduction of chemical labels into biomolecules is of utmost importance in chemical biology research. However, methods for selective chemical labeling of in vitro transcribed RNA are scarce. Herein, we describe experimental details for direct labeling of the 5'-phosphate of RNA using a diazo biotin-reagent, as exemplified on a 110 nucleotide RNA obtained via in vitro transcription. The method exploits the fact that, under neutral buffer conditions (~pH 6.8), the 5'-phosphate carries the only mildly acidic proton in the RNA molecule, which allows for selective functionalization at that site using diazo reagents.
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Affiliation(s)
- Greggory M Rice
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Razvan Nutiu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
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