Glycome : the hidden code in biology / edited by Dipak K. Banerjee.

Format:

Book

Contributor:

Banerjee, Dipak K., editor.

Series:

Biochemistry Research Trends

Language:

English

Subjects (All):

Glycomics.

Physical Description:

1 online resource (438 pages) : illustrations

Place of Publication:

New York, New York : Nova Science Publishers, Incorporated, [2021]

Summary:

"Glycome: The Hidden Code in Biology addresses one of the most fundamental questions in biology today. The book targets readers with little expertise as well as the experts in Glycoscience. Sugars are electroneutral. However, linking sugars to sugars, or attaching sugars to proteins or lipids changes the structural and functional identities of the glycoconjugate, and enables to form cellular networks of 4Gs [i.e., glycoproteins (N-linked or O-linked), glycosphingolipids, proteoglycans and glycosaminoglycans (GAGs)]. These glycans (i) support growth, proliferation and differentiation of cells and tissues; (ii) protect cells from foreign invasions including bacteria, viruses, parasites as well as from changes in the extracellular environment; (iii) act as biomarkers and participate in transmembrane signaling. The glycans are not ubiquitous but they are tissue/species specific. Structurally, the glycans are diverse, and form linear to highly branched structures. This diversity is present not only across the species but also within cells of the same species, i.e., the glycoforms. Nuclear magnetic resonance (NMR) and mass spectrometric (MS) studies (i.e., Glycomics) have evaluated and contributed significantly in delineating the structural diversity of glycans. Glycomics, in fact, has helped in overcoming many earlier technological barriers which were otherwise very laborious and time consuming. Plant lectins being carbohydrate binding proteins with a high degree of sugar specificity have been useful tools to characterize the carbohydrate structures they recognize. The glycan structures complement their biosynthetic processes. Because of the highly compartmentalized nature of the process, the glycans move between compartments during their assembly. This is believed to be mediated by vesicular structures but the participation of exosomes cannot be ruled out. A large number of genetic disorders [gangliosidosis, mucopolysaccharidoses, congenital disorders of glycosylation (CDG)] are due to abnormal glycan synthesis or degradation. Disproportionate expression of glycans is also found in diseases like cancer, neurological disorders, diabetes, metabolic syndromes, and infection. This raises questions about the regulatory principle(s) in glycan biosynthesis. There is no template for glycan chain synthesis, elongation, processing or termination. The cells/tissues follow a highly conserved mechanism. The assumption is glycosylation uses donor and acceptor interactions as the driving force. Increased or decreased synthesis of glycans in response to the environmental change influence cell function, i.e., growth, survival or death favor of a "push-pull" hypothesis. In the absence of a genetic code for sugars, the assembly as well as the processing of glycan chains are controlled by the Glycome. Unlike the genome, the Glycome is hidden for the normal eye but its communication skills with the cellular microenvironment and genome for glycan synthesis and degradation are enormous. Seventeen chapters in the book are dedicated to walk the readers through the diversities of the Glycome. The authors have used mammalian, microbial and plant systems to achieve the desired goal"-- Provided by publisher.

Contents:

Intro

Contents

Preface

Acknowledgements

Acronyms

Chapter 1

Interactome Facilitates Activation of Glycome Code for Asparagine-Linked Protein Glycosylation

Abstract

Abbreviations

Introduction

Function of N-Linked Glycans

Biosynthesis of Asparagine-Linked Glycoproteins

Assembly of Glc3Man9GlcNAc2-PP-Dolichol (LLO)

Regulation of LLO Biosynthesis

(a) Regulation from within (Cytosol v/s ER)

(b) Regulation by Extra-Cellular Environment

Interactome Facilitates Decoding Glycome (A Cross-Talk between DPMS and the GPT)

Decoding of Glycome by Dol-P-Man

Partial Reduction of DPMS Activity Does not Induce Apoptosis

Summary and Conclusion

Acknowledgments

References

Chapter 2

Oligosaccharides, Oligosaccharyl Phosphates and Congenital Disorders of Glycosylation

1. Introduction

2. Protein N-Glycosylation

2.1. Production of N-Glycans

2.1.1. Biosynthesis of DLO

2.1.1.1. Enzymes of the Dolichol Cycle

2.1.1.2. The Membrane Topology of the Dolichol Cycle and Transbilayer Movement of Lipid Carriers Biosynthesis of DLO

2.1.2. Transfer of Oligosaccharides onto Protein by OST

2.1.3. Biosynthesis of Dolichol and Recycling of Dolichyl Diphosphate in the ER

2.2. Mechanisms Regulating the Quantity and Quality DLO

2.2.1. DLO Regulation by Hydrolysis

2.2.1.1. Oligosaccharyltransferase-Mediated Generation of fOS from DLO

2.2.1.2. Hydrolysis of DLO to Yield Oligosaccharyl Phosphates (OSP)

3. Congenital Disorders of Glycosylation

3.1. CDG-I

3.1.1. Clinical Presentation of CDG-I

4. Advances in the Understanding of DLO Hydrolytic Mechanisms through Studies in Rare Inherited Glycosylation Diseases

4.1. OSP Production in CDG-I

4.2. The Search for OSP Generating Enzymes

4.3. fOS Production in PMM2-CDG.

4.4. fOS Production and TREX1 Deficiencies

General Conclusion and Future Perspectives

Acknowledgments/Grant Support

Chapter 3

Role of Inflammation in the Regulation of Epithelial Cell O-Glycosylation

2. Structure and Biosynthesis of Mucin-Type O-Glycans

2.1. Initiation of Mucin-Type O-Glycan Chains

2.2. Core structures Biosynthesis

2.3. Elongation of Mucin-Type O-Glycan Chains

2.4. Termination of Mucin-Type O-Glycan Chains

2.5. Sulfation of Mucin-Type O-Glycan Chains

3. Regulation of Glycosyltransferases and Sulfotransferases by Pro-Inflammatory Cytokines

4. Role in Inflammation in the Regulation of O-Glycosylation in Cystic Fibrosis

4.1. Modifications of Mucin Glycosylation and Sulfation in CF: Influence on P. aeruginosa Adhesion

4.2. Characteristics of Inflammatory Response in Cystic Fibrosis

4.3. Influence of Pro-Inflammatory Cytokines on the Expression and Activity of GTs and SulfoTs in Human Airways

5. Role in Inflammation in the Regulation of O-Glycosylation in Intestinal Bowel Diseases

Chapter 4

The O-GlcNAc Modification in Physiology and Disease

1. O-GlcNAcylation: A Brief History

2. O-GlcNAc Cycling and Evolution

2.1. OGT and Related Monosaccharyltransferases

2.2. O-GlcNAcase: Evolution of O-GlcNAc Cycling in Animals

3. Enymes of O-GlcNAc Cycling: From Genes and Regulation To Structure and Catalytic Mechanisms

3.1. O-GlcNAc Transferase (OGT)

3.2. O-GlcNAcase (OGA)

4. Hexosamine Biosynthetic Pathway

5. O-GlcNAcylated Targets

6. O-GlcNAc Deregulation and Disease

6.1. Immunity/Autoimmunity

6.2. Insulin Resistance/Diabetes

6.3. Neurodegeneration

6.4. Cancer

6.5. Cardiac Disease

7. Extracellular O-GlcNAc.

8. O-GlcNAcylation: A Final Summary

Chapter 5

Polysialic Acid as an Integrative Decoder in Nervous and Reproductive Systems

2. Polysialic Acid in Fertilization

2.1. Flagellasialin in Sperm Motility

2.2. Poly/OligoSia in Egg Coat Glycoconjugates

2.3. DiSia-Gangliosides in Sperm-Egg Envelope Attachment

2.4. Polysialoglycoproteins in Egg Cortical Reaction

2.5. Significance of PolySia-Glycans in Fertilization

3. Polysialic Acid in Neural System

3.1. Distribution of PolySia in Brain

3.2. Biochemical Properties of PolySia and Their Functions in Brain

3.3. Repulsive Field of PolySia

3.4. Attractive Field of PolySia

3.4.1. Neurotrophic Factors

3.4.2. Growth Factors

3.4.3. Neurotransmitters

3.4.4. Ions

3.5. Regulatory Role for Receptors

3.5.1. Ion Channel

3.5.2. Siglecs

4. Polysialic Acid in Diseases

4.1. Expression of PolySia in Brain Disorders

4.2. PolySia-Related Genes in Brain Disorders

4.2.1. SCZ and ST8SIA2

4.2.2. BD and ST8SIA2

4.3. PolySia-Expression Caused by Environmental Factors

Conclusion

Chapter 6

Decoding of (-Dystroglycan Glycosylation and Muscular Dystrophy

2. Dystroglycan

3. Structure and Function of O-Mannosyl Glycan

4. Biosynthesis of O-Mannosyl Glycan

4.1. Protein O-Mannosylation

4.2. Core M1 and Core M2 Biosynthesis

4.3. Core M3 Biosynthesis

5. Defects of O-Mannosyl Glycan and Congenital Muscular Dystrophies

Conclusion and Future Directions

Chapter 7

The Structure of Glycosphingolipid Oligosaccharides Hides a Specific Code for Protein Recognition

The Interaction of Gangliosides with Enzymatic Proteins.

The Interaction of Gangliosides with Membrane Receptors

Trk Receptor

EGF Receptor

Insulin Receptor

Chapter 8

Stereo-Specific Glycomic Codes of the Normal and Metastatic Cancer Cell Surfaces: Biosynthetic Pathways of Glycosphingolipids and Its Probable Biological Functions

2. Results and Discussion

2.1. Biosythesis of Brain Gangliosides with Gg-Glycome-epitope

2.2. Distribution of Different Ceramide-Glycomes on the RBC of Different Species

2.3. Biosynthesis of Gb-Family Glyco-Epitopes (Gal-α1-4-Gal-β1-4Glcβ1-1Cer) of Blood Cell Surface origin

2.4. Biosynthesis of Various Blood Group-Types in Spleen and Bone Marrow Cells starting from nLcose4-CER Epitope intermediate

2.5. Biosynthesis of Higher Cer-Glycomes containing nLcOse4-Cer

2.6. Modulation of Acidic Glycosphingolipid Biosynthesis during Apoptosis

2.7. Oligoglycome Glycosphingolipids found in Organs of Different Species and Probable Functional Roles for its Stereo-specificity

2.8. Characterization of Radioactive -Products (containing 14C-or 3H-Glycome-Ceramide) by Microimmunodiffusion methods established by Sen-itiroh Hakomori

Acknowledgment

Chapter 9

Carbohydrates in Health and Disease: A Plant's Perspective

Plant Carbohydrates

At the Cell Wall

In the Cytoplasmic Compartment

Role of Carbohydrate Structures in Growth and Development

Importance of N-Glycosylation for Plant Development and Abiotic Stress Signaling

Importance of O-Glycosylation for Plant Development and Abiotic Stress Signaling

Importance of Carbohydrate Structures for Plant-Pathogen Interactions

Role of Protein-Carbohydrate Interactions in Defense, Growth and Development

Carbohydrate Interactions with Membrane-Associated Lectins.

Carbohydrate Interactions with Lectins in the Nucleus and Cytoplasm

Future Challenges

Chapter 10

New Paradigm for Chronic Inflammation Mediated by GM3 Ganglioside Molecular Species

2. GM3 Functions as a Physiological Regulator for Insulin Signaling and Adipogenesis

3. Pathogenic Control of Adipocytes by the Increased Expression of GM3

4. Pro- and Anti-Inflammatory Activities of GM3 Molecular Species in Human Sera

5. Selective Modulation of Human TLR4/MD-2 Signaling by GM3 Molecular Species

6. Homeostatic Balance and Pathogenic Alteration of Serum GM3 Species Involved in Chronic Inflammation

7. GM3 Species with Proinflammatory Activity Increase in Adipose Tissue in Metabolic Disorders

8. Molecular Basis for GM3-Species Recognition by TLR4/MD-2 Complex

9. Metabolic and Biosynthetic Pathway of GM3 Species with Pro-/Anti-Inflammatory Activity

Chapter 11

Glycans as Gastrointestinal Cancer Biomarkers: Old and New Diagnostic, Predictive and Stratifying Tools

1. Glycosylation in Homeostasis : A Finely-Tuned Molecular Symphony

2. Glycosylation Landscape of the Human Gastrointestinal Tract: Dynamic Spatiotemporal Regulation

3. Glycosylation Changes in Gastrointestinal Malignancy: Diagnostic and Prognostic Utility

4. Molecular Subtyping of Gastrointestinal Cancer: Glycans as an Additional Layer of Tumor Heterogeneity

5. Protein Targets of Abnormal Glycosylation in Gastrointestinal Cancer: A Mechanistic View

6. Novel Glycoconjugate Signatures as Reliable Gastrointestinal Tumor Biomarkers

Conclusion: Putting Glycans in the Context of Precision Medicine

Chapter 12.

Development of a Comprehensive Heparan Sulfate Mutant Cell Library and Its Application to Determine the Structure-Function Relation of Heparan Sulfate in Regulation of FGF2-FGFR1 Signaling.

Notes:

Description based on print version record.

Includes bibliographical references and index.

ISBN:

1-5361-9437-9

OCLC:

1246583307