- Email: [email protected]
Exploring Glycans
Cell 150
approaches have been applied to the parallel identification of the subunits of multiprotein complexes (e.g., snRNP, Neubauer et al., Proc. Natl. Acad. Sci. USA 94, 385–390, 1997) or their substrates (e.g., GroEL, Houry et al., Nature 402, 147–154, 1999). In perhaps the most extreme example, libraries of mouse mutants are now being made and phenotyped in a manner once restricted to simpler organisms. Projects that once required the dedication of an obsessive post-doc or graduate student are now high throughput and routine. The implication is that entirely new data formats will be generated in sufficient quantities to be labeled as databases. There are a few minor criticisms concerning organization of the book. The chapters vary somewhat in their format: some briefly describe the content of a catalog of URLs on a particular subject, while others are more theoretical. One of the chapters contains exercises, as if written for teaching purposes; the others do not. They are also presented in a rather confusing order with some redundancy. Another disappointment is the lack of any supporting internet content: at the least, a companion web page or bookmark folder would have been more useful than the six pages of URLs listed in an appendix. In fact, it is debatable whether this collection of reviews would have been better published on the internet rather than on paper; these are fast-moving fields and their description would benefit from frequent updates and hyperlinking. It is probably a measure of how much we expect our internet content to be free that publishing books describing it is still popular. That said, there is much in the book to commend. There are few resources, online or otherwise, that describe the diversity of online databases in this way. Most of the chapters are well written and the points raised are often illustrated by examples, making the arguments easy to follow for a nonexpert. Perhaps of most significant consequence for the average reader is that the “black box” approach to database searching will seem less tempting when simple explanations for the algorithms acting behind the scenes are available in such a compact volume. G. Williams closes his chapter on nucleic acid and protein databases with the message “If you get anomalous results, stop and think for a while” (page 36). It will also help to pick up this book. Richard Glynne Eos Biotechnology, Inc. 225a Gateway Boulevard South San Francisco, California 94080
Exploring Glycans Essentials of Glycobiology By A. Varki, R. Cummings, J. Esko, H. Freeze, G. Hart, and J. Marth Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press (1999). 668 pp. $95.00 Scientific disciplines pass through distinct developmental stages. The initial, “Linnean” phase entails the
identification and classification of the essential elements. For glycobiology, this phase of determining the structure and elucidating biosynthesis pathways of natural carbohydrates or glycans has been quite long. Numerous glycobiologists are still working on the isolation and biochemical analysis of glycans and glycoconjugates (glycoproteins and glycolipids), and the identification of the multitude of enzymes involved in their biosynthesis, modification, and degradation. This is necessary and justifiable given the extraordinary diversity and heterogeneity of these molecules and the complexity of the biosynthetic process. The work continues to be demanding because the methodology available to analyze complex polysaccharides is cumbersome and technically difficult. Nevertheless, as illustrated by the newly published book, Essentials of Glycobiology, the field is well on its way into the next stage, a phase that addresses functions and mechanisms. As the book demonstrates, the study of carbohydrates is increasingly connected to cell biology, structural biology, molecular genetics, medicine, and other disciplines. As a result of interdisciplinary efforts, a more comprehensive picture is emerging of the functions that carbohydrates play at the molecular, cellular, and organismal level. Nature makes use of carbohydrates in rich and multifaceted ways. Polysaccharides and glycoconjugates are essential components of the extracellular matrix and other structures in the intercellular space, and are therefore essential for tissue structure and cell interactions in multicellular organisms. They are also modulators of protein folding, determinants of intra-cytosolic sorting, signals for recognition, and “diversity generators” in cell–cell interactions. They serve as receptors for toxins and pathogens, as antifreeze agents, as species–specific receptors during fertilization, as energy storage molecules, as raft-generating components of membranes, and as other diverse biological effectors. In archaea, bacteria, fungi, and plants, the cell wall, mainly composed of carbohydrates, provides a dynamic yet exceptionally robust protective capsule. For the experimentalist trying to approach glycans in the context of their cellular functions, the major problem is that the DNA→RNA→protein paradigm cannot be extended to glycans. This is because glycan synthesis occurs without a template derived directly from genes. Structure and composition is determined by complex batteries of biosynthetic enzymes working mainly within the ER, the Golgi complex, or in specialized factories in the plasma membrane. Regulation of glycan synthesis occurs through subtle changes in the activities of biosynthetic and catalytic machinery. Built into the biosynthetic machinery is the production of a spectra of microheterogeneties during glycan synthesis. In spite of the apparent randomness in glycan biosynthesis, the regulation of these processes is exquisitely specific. While some polysaccharides and glycoconjugates display extensive heterogeneity, other glycan additions are amazingly reproducible, illustrated by the precise shapes of plant pollen and by the delicate control of bud formation in yeasts. Essentials of Glycobiology should be required reading for any biologist aspiring to understand the molecular basis of cell and tissue function. It provides an excellent introduction into carbohydrate biology for a novice, and
Book Reviews 151
it will be useful for university level teachers seeking additional breadth to their courses in biochemistry or cell biology. In easily understood fashion, it describes the basic properties of various types of glycans and glycoconjugates. Well-designed figures help the reader understand the complex structures. A major part of the book is devoted to the biosynthesis and the metabolism of N- and O-linked oligosaccharides in proteins, glycosphingolipids, GPI-anchors, proteoglycans, and glycosaminoglycans. Lectins and the increasingly detailed structural understanding of protein–carbohydrate interactions are covered in several detailed chapters. There are also helpful chapters on the structural analysis and chemical synthesis of glycans. For someone already working in the area, the book’s main value is its emphasis on the interfaces with cell biology, molecular biology, parasitology, medicine, and other fields. The book provides valuable background information about the present state of knowledge regarding carbohydrates in model organisms such as Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans. The use of transgenic mouse technology to investigate the functions of oligosaccharide structures is discussed in a separate chapter. This information will be increasingly relevant for addressing glycan functions in more detail. Only in genetically accessible model systems that allow deletion or insertion of specific glycosyltransferases or glycosidases is it possible to tailor the structure of specific glycans. Already, mutant mice are serving as models for several human diseases involving defects in glycan metabolism such as carbohydrate-deficient glycoprotein syndrome (CDGS) and chronic glomerulonephritis. What are the most interesting current issues in glycobiology? To us, there are several. Some of them are adequately described in the book, others need more attention in future editions. The Golgi Complex as a Biosynthetic Organelle. The Golgi complex is the main generator of glycan diversity in eukaryotic cells. It houses a large assortment of glycosyltransferases, glycosidases and other enzymes needed for oligosaccharide synthesis and modification. It will be necessary to learn more about the cell biology and physiology of this organelle, and the principles that govern the interaction between the different glycosyltransferases, and between these enzymes and their substrates. The Role of Glycans in Protein Folding. N-linked glycans are essential for the efficient folding of many glycoproteins in the ER. They affect folding directly by modifying the properties of the polypeptide chains, and indirectly by allowing the proteins to interact with lectins and folding sensors. The latter systems promotes folding, mediate quality control and, in the case of misfolding, targets glycoproteins for retrotranslocation to the cytosol and degradation. The underlying pathways and concepts remain inadequately understood. The Role of Glycolipids. It is increasingly clear that the diversity of lipid species in the cell is explained by each lipid family having distinct functions. This seems also to be true for glycosphingolipids. More detailed analysis is needed to determine their precise role in “rafts” and other specialized membrane domains. O-GlcNAc Modification of Cytosolic and Nuclear Proteins. This reversible, posttranslational modification of
Figure 1. Electron Microscopy of the Cell Wall in S. cerevisiae A section through the 150 nm–thick cell wall reveals several distinct layers composed of glycans and glycoproteins. The image was obtained after high pressure freezing and freeze substitution. (Figure courtesy of Dr. Martin Mu¨ller, Laboratory for Electron Microscopy, Swiss Federal Institute of Technology.)
serine and threonine residues is commonly observed in proteins of the nuclear pore complex, cytoskeleton, and chromatin. It appears to mask phosphorylation sites, and is thus likely to be involved in cell regulation. The Synthesis of Cell Walls. The synthesis and modulation of the cell wall in plants, fungi, bacteria, or archaea constitutes a fascinating field of research. Glycans are the major components of these robust, architecturally complex extracellular structures (Figure 1). While providing a strong framework, they are at the same time able to grow and divide with the cell, and to allow the cell to interact with the environment. The biogenesis of the cell wall remains a target for urgently needed novel antibiotics or fungicides. Evolutionary Aspects. Like other macromolecules, all glycans have evolved from structures present in simple bacteria. By analyzing in more detail the evolutionary relationships, valuable new information can be obtained. Essentials of Glycobiology is one of the first books to have the newly coined term “glycobiology” in its title. The authors succeed in giving the word a specific context without being too limiting. They also make clear that through new model systems and recent methodological and conceptual advances, the field is gaining momentum and recognition. New investigators are entering with novel questions and insights. At a deeper level, this book may also help newcomers and other interested readers to appreciate the mind-set needed for thinking constructively about glycans, and for approaching this “last frontier” of biochemistry and cellular biology. Ari Helenius and Markus Aebi Institute of Biochemistry and Institute of Microbiology Swiss Federal Institute of Technology (ETHZ) Zu¨rich, Switzerland
approaches have been applied to the parallel identification of the subunits of multiprotein complexes (e.g., snRNP, Neubauer et al., Proc. Natl. Acad. Sci. USA 94, 385–390, 1997) or their substrates (e.g., GroEL, Houry et al., Nature 402, 147–154, 1999). In perhaps the most extreme example, libraries of mouse mutants are now being made and phenotyped in a manner once restricted to simpler organisms. Projects that once required the dedication of an obsessive post-doc or graduate student are now high throughput and routine. The implication is that entirely new data formats will be generated in sufficient quantities to be labeled as databases. There are a few minor criticisms concerning organization of the book. The chapters vary somewhat in their format: some briefly describe the content of a catalog of URLs on a particular subject, while others are more theoretical. One of the chapters contains exercises, as if written for teaching purposes; the others do not. They are also presented in a rather confusing order with some redundancy. Another disappointment is the lack of any supporting internet content: at the least, a companion web page or bookmark folder would have been more useful than the six pages of URLs listed in an appendix. In fact, it is debatable whether this collection of reviews would have been better published on the internet rather than on paper; these are fast-moving fields and their description would benefit from frequent updates and hyperlinking. It is probably a measure of how much we expect our internet content to be free that publishing books describing it is still popular. That said, there is much in the book to commend. There are few resources, online or otherwise, that describe the diversity of online databases in this way. Most of the chapters are well written and the points raised are often illustrated by examples, making the arguments easy to follow for a nonexpert. Perhaps of most significant consequence for the average reader is that the “black box” approach to database searching will seem less tempting when simple explanations for the algorithms acting behind the scenes are available in such a compact volume. G. Williams closes his chapter on nucleic acid and protein databases with the message “If you get anomalous results, stop and think for a while” (page 36). It will also help to pick up this book. Richard Glynne Eos Biotechnology, Inc. 225a Gateway Boulevard South San Francisco, California 94080
Exploring Glycans Essentials of Glycobiology By A. Varki, R. Cummings, J. Esko, H. Freeze, G. Hart, and J. Marth Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press (1999). 668 pp. $95.00 Scientific disciplines pass through distinct developmental stages. The initial, “Linnean” phase entails the
identification and classification of the essential elements. For glycobiology, this phase of determining the structure and elucidating biosynthesis pathways of natural carbohydrates or glycans has been quite long. Numerous glycobiologists are still working on the isolation and biochemical analysis of glycans and glycoconjugates (glycoproteins and glycolipids), and the identification of the multitude of enzymes involved in their biosynthesis, modification, and degradation. This is necessary and justifiable given the extraordinary diversity and heterogeneity of these molecules and the complexity of the biosynthetic process. The work continues to be demanding because the methodology available to analyze complex polysaccharides is cumbersome and technically difficult. Nevertheless, as illustrated by the newly published book, Essentials of Glycobiology, the field is well on its way into the next stage, a phase that addresses functions and mechanisms. As the book demonstrates, the study of carbohydrates is increasingly connected to cell biology, structural biology, molecular genetics, medicine, and other disciplines. As a result of interdisciplinary efforts, a more comprehensive picture is emerging of the functions that carbohydrates play at the molecular, cellular, and organismal level. Nature makes use of carbohydrates in rich and multifaceted ways. Polysaccharides and glycoconjugates are essential components of the extracellular matrix and other structures in the intercellular space, and are therefore essential for tissue structure and cell interactions in multicellular organisms. They are also modulators of protein folding, determinants of intra-cytosolic sorting, signals for recognition, and “diversity generators” in cell–cell interactions. They serve as receptors for toxins and pathogens, as antifreeze agents, as species–specific receptors during fertilization, as energy storage molecules, as raft-generating components of membranes, and as other diverse biological effectors. In archaea, bacteria, fungi, and plants, the cell wall, mainly composed of carbohydrates, provides a dynamic yet exceptionally robust protective capsule. For the experimentalist trying to approach glycans in the context of their cellular functions, the major problem is that the DNA→RNA→protein paradigm cannot be extended to glycans. This is because glycan synthesis occurs without a template derived directly from genes. Structure and composition is determined by complex batteries of biosynthetic enzymes working mainly within the ER, the Golgi complex, or in specialized factories in the plasma membrane. Regulation of glycan synthesis occurs through subtle changes in the activities of biosynthetic and catalytic machinery. Built into the biosynthetic machinery is the production of a spectra of microheterogeneties during glycan synthesis. In spite of the apparent randomness in glycan biosynthesis, the regulation of these processes is exquisitely specific. While some polysaccharides and glycoconjugates display extensive heterogeneity, other glycan additions are amazingly reproducible, illustrated by the precise shapes of plant pollen and by the delicate control of bud formation in yeasts. Essentials of Glycobiology should be required reading for any biologist aspiring to understand the molecular basis of cell and tissue function. It provides an excellent introduction into carbohydrate biology for a novice, and
Book Reviews 151
it will be useful for university level teachers seeking additional breadth to their courses in biochemistry or cell biology. In easily understood fashion, it describes the basic properties of various types of glycans and glycoconjugates. Well-designed figures help the reader understand the complex structures. A major part of the book is devoted to the biosynthesis and the metabolism of N- and O-linked oligosaccharides in proteins, glycosphingolipids, GPI-anchors, proteoglycans, and glycosaminoglycans. Lectins and the increasingly detailed structural understanding of protein–carbohydrate interactions are covered in several detailed chapters. There are also helpful chapters on the structural analysis and chemical synthesis of glycans. For someone already working in the area, the book’s main value is its emphasis on the interfaces with cell biology, molecular biology, parasitology, medicine, and other fields. The book provides valuable background information about the present state of knowledge regarding carbohydrates in model organisms such as Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans. The use of transgenic mouse technology to investigate the functions of oligosaccharide structures is discussed in a separate chapter. This information will be increasingly relevant for addressing glycan functions in more detail. Only in genetically accessible model systems that allow deletion or insertion of specific glycosyltransferases or glycosidases is it possible to tailor the structure of specific glycans. Already, mutant mice are serving as models for several human diseases involving defects in glycan metabolism such as carbohydrate-deficient glycoprotein syndrome (CDGS) and chronic glomerulonephritis. What are the most interesting current issues in glycobiology? To us, there are several. Some of them are adequately described in the book, others need more attention in future editions. The Golgi Complex as a Biosynthetic Organelle. The Golgi complex is the main generator of glycan diversity in eukaryotic cells. It houses a large assortment of glycosyltransferases, glycosidases and other enzymes needed for oligosaccharide synthesis and modification. It will be necessary to learn more about the cell biology and physiology of this organelle, and the principles that govern the interaction between the different glycosyltransferases, and between these enzymes and their substrates. The Role of Glycans in Protein Folding. N-linked glycans are essential for the efficient folding of many glycoproteins in the ER. They affect folding directly by modifying the properties of the polypeptide chains, and indirectly by allowing the proteins to interact with lectins and folding sensors. The latter systems promotes folding, mediate quality control and, in the case of misfolding, targets glycoproteins for retrotranslocation to the cytosol and degradation. The underlying pathways and concepts remain inadequately understood. The Role of Glycolipids. It is increasingly clear that the diversity of lipid species in the cell is explained by each lipid family having distinct functions. This seems also to be true for glycosphingolipids. More detailed analysis is needed to determine their precise role in “rafts” and other specialized membrane domains. O-GlcNAc Modification of Cytosolic and Nuclear Proteins. This reversible, posttranslational modification of
Figure 1. Electron Microscopy of the Cell Wall in S. cerevisiae A section through the 150 nm–thick cell wall reveals several distinct layers composed of glycans and glycoproteins. The image was obtained after high pressure freezing and freeze substitution. (Figure courtesy of Dr. Martin Mu¨ller, Laboratory for Electron Microscopy, Swiss Federal Institute of Technology.)
serine and threonine residues is commonly observed in proteins of the nuclear pore complex, cytoskeleton, and chromatin. It appears to mask phosphorylation sites, and is thus likely to be involved in cell regulation. The Synthesis of Cell Walls. The synthesis and modulation of the cell wall in plants, fungi, bacteria, or archaea constitutes a fascinating field of research. Glycans are the major components of these robust, architecturally complex extracellular structures (Figure 1). While providing a strong framework, they are at the same time able to grow and divide with the cell, and to allow the cell to interact with the environment. The biogenesis of the cell wall remains a target for urgently needed novel antibiotics or fungicides. Evolutionary Aspects. Like other macromolecules, all glycans have evolved from structures present in simple bacteria. By analyzing in more detail the evolutionary relationships, valuable new information can be obtained. Essentials of Glycobiology is one of the first books to have the newly coined term “glycobiology” in its title. The authors succeed in giving the word a specific context without being too limiting. They also make clear that through new model systems and recent methodological and conceptual advances, the field is gaining momentum and recognition. New investigators are entering with novel questions and insights. At a deeper level, this book may also help newcomers and other interested readers to appreciate the mind-set needed for thinking constructively about glycans, and for approaching this “last frontier” of biochemistry and cellular biology. Ari Helenius and Markus Aebi Institute of Biochemistry and Institute of Microbiology Swiss Federal Institute of Technology (ETHZ) Zu¨rich, Switzerland