Fukuda Glycobiology

1. Auflage 2010
ISBN: 978-0-12-381000-7
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, Band Volume 480, 640 Seiten

Reihe: Methods in Enzymology

In this 3 volume collection focusing on glycomics, readers will appreciate how such discoveries were made and how such methods can be applied for readers' own research efforts - Each chapter has been designed so that enough scientific background will be given in each chapter for further development of methods by readers themselves - Useful for all levels of scientists starting from the last years of colleges, graduate students, postdoctoral fellows to professors and to all levels of scientists in research institutes including industry

Autoren/Hrsg.

Fukuda, Minoru

Inhaltsverzeichnis

1;Front Cover;1
2;Methods in Enzymology: Glycobiology;4
3;Copyright Page;5
4;Contents;6
5;Contributors;16
6;Preface;24
7;Methods in Enzymology;26
8;Section One: Proteoglycans and Sulfotransferases;54
8.1;Chapter One: Auxiliary and Autonomous Proteoglycan Signaling Networks;56
8.1.1;Abstract;56
8.1.2;1. Overview of Proteoglycan Structure, Nomenclature, and Function;57
8.1.3;2. Growth Factor Signaling;58
8.1.4;3. Integrin Interactions;59
8.1.5;4. Autonomous Signaling;59
8.1.6;5. Proteoglycan Downregulation: Endocytosis and Ectodomain Shedding;62
8.1.7;6. Cell Adhesion;63
8.1.8;7. Migration;67
8.1.9;8. Experimental Procedures;70
8.1.10;Acknowledgments;81
8.1.11;References;82
8.2;Chapter Two: Dual Roles of Drosophila Glypican Dally-Like in Wingless/Wnt Signaling and Distribution;86
8.2.1;Abstract;87
8.2.2;1. Introduction;87
8.2.3;2. Generation of Dally and Dlp Null Alleles;88
8.2.4;3. Examination of Dally and Dlp in Wg Signaling and Gradient Formation in the Wing Disc;89
8.2.5;4. Dlp Core Protein Determines Its Biphasic Activity in Wg Morphogen Signaling;92
8.2.6;5. Dlp Core Protein Can Interact with Wg Independent of Its GAG Chains;95
8.2.7;6. The Ratio of Dlp/Fz2 Determines the Biphasic Activity of Dlp or Dlp Core Protein in Wg Signaling;99
8.2.8;7. Conclusion;101
8.2.9;Acknowledgments;101
8.2.10;References;102
8.3;Chapter Three: Use of a Phage Display Antibody to Measure the Enzymatic Activity of the Sulfs;104
8.3.1;Abstract;104
8.3.2;1. Overview;105
8.3.3;2. ELISA for Sulf Activity Against the RB4CD12 Epitope in Immobilized Heparin/HS;107
8.3.4;3. Flow Cytometry-Based Sulf Assay Against the Cell Surface RB4CD12 Epitope;108
8.3.5;4. Ex Vivo Sulf Assay Against the RB4CD12 Epitope in Cryostat-Cut Sections;112
8.3.6;Acknowledgments;115
8.3.7;References;115
8.4;Chapter Four: Glycomics Profiling of Heparan Sulfate Structure and Activity;118
8.4.1;Abstract;118
8.4.2;1. Overview;119
8.4.3;2. Experimental;122
8.4.4;3. Conclusions and Future Perspectives;134
8.4.5;Acknowledgments;134
8.4.6;References;134
9;Section Two: Lectins, Immunity and Infection;140
9.1;Chapter Five: Microbe-Associated Molecular Patterns in Innate Immunity;142
9.1.1;Abstract;143
9.1.2;1. Overview;144
9.1.3;2. LPS and LOS Extraction Procedures;146
9.1.4;3. Purification of the Crude Extracts;149
9.1.5;4. SDS-PAGE;151
9.1.6;5. Carbohydrate Analysis: Monosaccharide Determination, Absolute Configuration, and Definition of Branching Points...;154
9.1.7;6. Fatty Acids Compositional Analysis (GC-MS);162
9.1.8;References;167
9.2;Chapter Six: Structural and Functional Analysis of Glycosphingolipids of Schistosoma mansoni;170
9.2.1;Abstract;171
9.2.2;1. Overview;171
9.2.3;2. Isolation and Purification of S. mansoni Glycosphingolipids;172
9.2.4;3. Structural Characterization of S. mansoni Glycosphingolipids;174
9.2.5;4. Immunochemical Characterization of Glycan Antigens;181
9.2.6;5. Interaction of S. mansoni Glycosphingolipids with Dendritic Cell Receptors;183
9.2.7;6. Conclusions;189
9.2.8;References;189
9.3;Chapter Seven: Biotoxicity Assays for Fruiting Body Lectins and Other Cytoplasmic Proteins;194
9.3.1;Abstract;194
9.3.2;1. Overview;195
9.3.3;2. Expression of Fruiting Body Lectins in E. coli;196
9.3.4;3. Toxicity Test Toward the Insect A. aegypti;198
9.3.5;4. Toxicity Test Toward the Nematode C. elegans;200
9.3.6;5. Toxicity Test Toward the Amoeba A. castellanii;200
9.3.7;6. Statistics;201
9.3.8;Acknowledgments;201
9.3.9;References;201
9.4;Chapter Eight: Carbohydrate Signaling by C-Type Lectin DC-SIGN Affects NF-kappaB Activity;204
9.4.1;Abstract;204
9.4.2;1. Overview;205
9.4.3;2. Dendritic Cell Stimulation with LPS and ManLAM;206
9.4.4;3. RNA Interference in Dendritic Cells;208
9.4.5;4. NF-kappaB Activation in DCs;209
9.4.6;5. Phosphorylation and Acetylation of NF-kappaB by DC-SIGN Signaling;210
9.4.7;6. Activity of Acetyltransferases in DC;213
9.4.8;7. Transcription Regulation by Acetylation of p65;214
9.4.9;8. Concluding Remarks;215
9.4.10;Acknowledgments;216
9.4.11;References;217
9.5;Chapter Nine: Engineered Carbohydrate-Recognition Domains for Glycoproteomic Analysis of Cell Surface Glycosylation and Ligands;218
9.5.1;Abstract;219
9.5.2;1. Overview;219
9.5.3;2. Engineering Glycan-Binding Specificity;220
9.5.4;3. CRDs as Probes for Detection of Glycans on Blots;224
9.5.5;4. CRDs as Affinity Tools for Probing of Cell Surface Glycosylation;225
9.5.6;Acknowledgments;231
9.5.7;References;231
9.6;Chapter Ten: Mannose 6-Phosphate Receptor Homology Domain-Containing Lectins in Mammalian Endoplasmic Reticulum-Associated Deg;234
9.6.1;Abstract;234
9.6.2;1. Overview;235
9.6.3;2. Quality Control of Newly Synthesized Glycoproteins;236
9.6.4;3. Primary Structures of Yos9p, OS-9, and XTP3-B;237
9.6.5;4. OS-9 and XTP3-B form a Complex with Membrane-Embedded Ubiquitin Ligase;240
9.6.6;5. Sugar Recognition Specificity of OS-9 and XTP3-B;243
9.6.7;6. The Effect of OS-9 and XTP3-B on ERAD in Mammals;244
9.6.8;7. Concluding Remarks;246
9.6.9;Acknowledgments;247
9.6.10;References;247
9.7;Chapter Eleven: Multiple Functional Targets of the Immunoregulatory Activity of Galectin-1;252
9.7.1;Abstract;253
9.7.2;1. General Introduction;253
9.7.3;2. Regulation of Immune Cell Trafficking, Recruitment, and Chemotaxis;255
9.7.4;3. Galectin-Glycan Lattices in the Control of DC Physiology;269
9.7.5;4. Galectin-Glycan Lattices in the Control of T Helper Cell Fate;282
9.7.6;5. Final Remarks and Future Directions;290
9.7.7;Acknowledgments;292
9.7.8;References;292
9.8;Chapter Twelve: Manipulating Cell Surface Glycoproteins by Targeting N-Glycan-Galectin Interactions;298
9.8.1;Abstract;298
9.8.2;1. Overview;299
9.8.3;2. Galectins and Their N-Glycan Ligands;299
9.8.4;3. Regulation of Glycoprotein Concentration at the Cell Surface by the Galectin-Glycoprotein Lattice;301
9.8.5;4. T Cells and the Galectin-Glycoprotein Lattice;302
9.8.6;5. Genetic and Metabolic Regulation of the Galectin-Glycoprotein Lattice;302
9.8.7;6. Overview of Methods to Measure and Modulate the Galectin-Glycoprotein Lattice;303
9.8.8;References;315
9.9;Chapter Thirteen: Galectin-1 and HIV-1 Infection;320
9.9.1;Abstract;320
9.9.2;1. Overview;321
9.9.3;2. Experimental;325
9.9.4;References;341
10;Section Three: Drosophila;348
10.1;Chapter Fourteen: The Glycomics of Glycan Glucuronylation in Drosophila melanogaster;350
10.1.1;Abstract;350
10.1.2;1. Introduction;351
10.1.3;2. Experimental Procedures and Results;353
10.1.4;3. Discussion;367
10.1.5;Acknowledgments;370
10.1.6;References;370
10.2;Chapter Fifteen: Glycosyltransferases and Transporters that Contribute to Proteoglycan Synthesis in Drosophila;376
10.2.1;Abstract;377
10.2.2;1. Overview of Glycosaminoglycan Biosynthesis in Drosophila;377
10.2.3;2. Identification of Drosophila Glycosyltransferases and Sugar-Nucleotide Transporters that Contribute to Proteoglycan Synthes;389
10.2.4;3. Establishment and Functional Analysis of RNAi Flies for the Glycosyltransferases and Sugar-Nucleotide Transporters that Con;393
10.2.5;References;399
11;Section Four: NOTCH Signaling;406
11.1;Chapter Sixteen: O-GlcNAc Modification of the Extracellular Domain of Notch Receptors;408
11.1.1;Abstract;408
11.1.2;1. Overview;409
11.1.3;2. Preparation of Recombinant EGF Domains by Yeast Expression System;411
11.1.4;3. In Vitro O-GlcNAc Transferase Assay;413
11.1.5;4. Mass Spectrometry;413
11.1.6;5. Detection of O-beta-GlcNAc Modification Using Antibodies;416
11.1.7;6. Galactosyltransferase Labeling;418
11.1.8;7. Hexosaminidase Treatment;420
11.1.9;8. Conclusions and Future Directions;422
11.1.10;Acknowledgments;423
11.1.11;References;423
11.2;Chapter Seventeen: Regulation of Notch Signaling Via O-Glucosylation;428
11.2.1;Abstract;429
11.2.2;1. Overview;429
11.2.3;2. Genetic Identification and Characterization of rumi;430
11.2.4;3. Drosophila Strains;432
11.2.5;4. Drosophila Culture and Husbandry;433
11.2.6;5. A Genetic Screen to Identify New Notch Regulators;434
11.2.7;6. Mapping and Sequencing;435
11.2.8;7. Rescue Experiments;437
11.2.9;8. Generation of a Protein-Null Allele of rumi Via P-Element Excision;438
11.2.10;9. Experimental Evidence that Rumi is a Protein O-Glucosyltransferase;439
11.2.11;10. Enzyme Assay for Protein O-Glucosyltransferase Activity;442
11.2.12;11. Analysis of the Product Obtained from the Protein O-Glucosyltransferase Assay;443
11.2.13;12. Detection of O-Linked Glucose on Notch EGF Repeats by Mass Spectrometry;445
11.2.14;Acknowledgments;448
11.2.15;References;448
12;Section Five: New Development;452
12.1;Chapter Eighteen: O-Fucosylation of Thrombospondin Type 1 Repeats;454
12.1.1;Abstract;454
12.1.2;1. Overview;455
12.1.3;2. Glycosylation Site Mapping by Mass Spectrometry;460
12.1.4;Acknowledgments;466
12.1.5;References;466
12.2;Chapter Nineteen: Use of Glycan Microarrays to Explore Specificity of Glycan-Binding Proteins;470
12.2.1;Abstract;470
12.2.2;1. Overview;471
12.2.3;2. The Printed Glycan Microarray from the Consortium for Functional Glycomics (CFG);472
12.2.4;3. Analysis of GBPs on the CFG Glycan Microarray;474
12.2.5;4. Defining a Glycan Motif Using Concentration-Dependent Binding of GBPs to the Printed Glycan Microarray;475
12.2.6;5. The Concentration-Dependent Binding of Sambucus nigra Agglutinin to the Printed Glycan Microarray and a Method for Ranking;476
12.2.7;6. Using Microarrays to Identify a Glycan-Binding Motif for SNA;478
12.2.8;7. Specificities of Human Galectin-8 and its Carbohydrate Recognition Domains (CRDs);484
12.2.9;8. Challenges in Identifying Physiological Ligands for GBPs;492
12.2.10;9. Conclusion and Future Directions;493
12.2.11;Acknowledgments;495
12.2.12;References;495
12.3;Chapter Twenty: Functional Roles of the Bisecting GlcNAc in Integrin-Mediated Cell Adhesion;498
12.3.1;Abstract;498
12.3.2;1. Overview;499
12.3.3;2. Manipulation of GnT-III and GnT-V Genes in Cancer Cells;501
12.3.4;3. Assays for Cell Spreading and Migration;502
12.3.5;4. Construction of Various Integrin a5beta1 Mutants by the Mutagenesis of Potential N-Glycos;504
12.3.6;5. N-Glycans Differentially Regulate Integrin-Mediated Cell Adhesion and Migration;505
12.3.7;6. Identification of Important N-Glycosylation Sites for Functional Expression of a5beta1 Int;507
12.3.8;7. Site-4 Is a Crucial N-Glycosylation Site on the a5 Subunit for GnT-III Regulation;508
12.3.9;8. Future Perspectives;509
12.3.10;Acknowledgments;509
12.3.11;References;509
12.4;Chapter Twenty-One: Lectin-Based Glycoproteomic Techniques for the Enrichment and Identification of Potential Biomarkers;514
12.4.1;Abstract;514
12.4.2;1. Introduction;515
12.4.3;2. Lectin Blotting and Separation of Total Glycoproteins in a Sample Using a Lectin(s) Immobilized on Paramagnetic Beads...;518
12.4.4;3. Separation of Glycoproteins Using a Lectin Immobilized on Paramagnetic Beads Prior to Mass Spectrometry-Based Shotgun Prote;520
12.4.5;4. Glycomics Strategy for Identifying Potential Glycoprotein Cancer Markers;524
12.4.6;5. MS/MS Data Analysis and Confirmation of Glycoprotein Glycosylation Differences When Results from Two Tissue Sources are Com;524
12.4.7;6. Conclusions;526
12.4.8;Acknowledgments;527
12.4.9;References;527
12.5;Chapter Twenty - Two: High-Throughput RNAi Screening for N-Glycosylation Dependent Loci in Caenorhabditis elegans;530
12.5.1;Abstract;530
12.5.2;1. Overview;531
12.5.3;2. N-glycosylation in C. elegans;532
12.5.4;3. RNAi in C. elegans;533
12.5.5;4. C. elegans Strains, Culturing and RNAi Methods;533
12.5.6;5. Genome-wide RNAi Screen;539
12.5.7;6. Discussion;542
12.5.8;References;545
12.6;Chapter Twenty - Three: The Acidic Environment of the Golgi Is Critical for Glycosylation and Transport;548
12.6.1;Abstract;548
12.6.2;1. Introduction;549
12.6.3;2. Reporter Proteins for Transport Monitoring;552
12.6.4;3. Establishment of Parent Cells for Screening Transport Mutant Cells;553
12.6.5;4. Transport Assay of Reporter Proteins;554
12.6.6;5. Application of Transport Assay;554
12.6.7;6. Mutagenesis;557
12.6.8;7. Selection of Mutant Cells;557
12.6.9;8. Measurement of Golgi pH;557
12.6.10;9. Analysis of Glycosylation Using Lectin Staining;559
12.6.11;10. Concluding Remarks;559
12.6.12;Acknowledgment;560
12.6.13;References;560
12.7;Chapter Twenty - Four: Enzymatic Synthesis of Lacto-N-Difucohexaose I Which Binds to Helicobacter pylori;564
12.7.1;Abstract;565
12.7.2;1. Overview;565
12.7.3;2. Synthesis of Lacto-N-triose II Using beta-1,3-N-Acetylglucosaminyltransferase;566
12.7.4;3. Synthesis of Lacto-N-tetraose by Transglycosylation Using beta-1,3-Galactosidase;568
12.7.5;4. Preparation of Recombinants FUT1 and FUT3;571
12.7.6;5. Synthesis of Lacto-N-fucopentaose I and Lacto-N-difucohexaose I with the Aid of Fucosyltransferases;573
12.7.7;Acknowledgments;575
12.7.8;References;575
12.8;Chapter Twenty - Five: The Drosophila 7-Pass Transmembrane Glycoprotein BOSS and Metabolic Regulation;578
12.8.1;Abstract;578
12.8.2;1. Introduction;579
12.8.3;2. BOSS: Drosophila Orphan Membrane Receptor;583
12.8.4;3. BOSS Responds to Extracellular Glucose;585
12.8.5;4. Sugar and Lipid Metabolism Is Impaired in boss Null Mutants;585
12.8.6;5. boss Mutant Flies Are Sensitive to Starvation;586
12.8.7;6. Biochemical Techniques for Detecting TAG;588
12.8.8;References;590
13;Author Index;592
14;Subject Index;622
15;Color Plates;636