Bacterial Glycomics: Current Research, Technology and Applications | Book
"an important reference book" (ASM Microbe)
Caister Academic Press
Christopher W. Reid, Susan M. Twine, and Anne N. Reid
Department of Science and Technology, Bryant University, Smithfield RI, USA; National Research Council Canada, Institute for Biological Sciences, Ottawa, Canada; Cumberland RI, USA (respectively)
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Glycomics, the study of glycoconjugate assembly and expression in biological systems, is important in many areas of microbiology. Because glycans play such diverse roles in bacterial physiology, the field of bacterial glycomics is indispensable for the understanding of bacterial pathogenesis, metabolism and cell communities. Progress in bacterial glycomics is advancing rapidly due to improvements in analytical methodologies and the development of new and innovative approaches for glycan isolation, characterization and synthesis. Research in bacterial glycomics could lead to the development of novel drugs, bioactive glycans and glycoconjugate vaccines.
Written by a team of acknowledged experts, this book provides an up-to-date overview of our current understanding of bacterial glycomes, describes the main analytical methods in use and discusses recent and novel applications. The book is divided into three sections. The first section includes overviews of microbial glyconjugates, lipopolysaccharide, capsular polysaccharide, lipoarabinomannan biosynthesis, cell wall metabolism, and glycosylation of bacterial and archaeal proteins. The second section reviews the analytical approaches used in the characterization of the bacterial glycome. The final section describes applications of bacterial glycomics, including metabolic oligosaccharide labeling, the synthesis of bioactive glycans and the potential for glycoconjugate vaccines.
Essential reading for microbiologists working in polysaccharide and carbohydrate research, the book is also recommended for carbohydrate experts, microbiologists, immunologists and researchers in many other fields of life sciences.
"This book covers a topic in bacterial pathogenesis that is not often covered ... should be essential to any scientist working in the area of bacterial pathogenesis." from Doodys
"an up-to-date overview" from IFIS
"provide(s) researchers from all disciplines with an overview of bacterial glycomics ... with a strong focus on Gram-negative bacteria and pathogens" from Beneficial Microbes (2012) 3: 166-167.
"This book brings this exciting new knowledge together alongside the more traditional and established areas of bacterial glycoconjugate research and provides an overarching review of our current understanding of the bacterial glycome ... Bacterial Glycomics is an important reference book that provides a timely and current review of the biochemical knowledge of the major components of the bacterial glycome ... this book will be of great interest to many researchers in the microbial fıeld." from ASM Microbe (2013) 8, 299-300.
Table of contents
1. Lipopolysaccharide Biosynthesis
Lipopolysaccharide (LPS) constitutes the major portion of the outer leaflet of the outer membrane and plays a major role in the physiology of Gram-negative bacteria. LPS can be divided into three structurally distinct regions: lipid A, core oligosaccharide and O-antigenic polysaccharide. Each of these regions as well as regulated modifications, are important in the overall functions of the LPS molecule. Synthesis of lipid A and the core oligosaccharide occurs in the cytoplasm and is separate from that of the O-antigenic polysaccharide. These two portions of the LPS molecule are then ligated in the periplasm prior to transport to the outer membrane. This chapter will describe the structure and cytoplasmic synthesis of LPS, modifications to these structures regulated by environmental conditions or phage-encoded genes, and the transfer of LPS to its final destination at the cell surface.
2. Biosynthesis of Capsular Polysaccharides and Exopolysaccharides
Anne N. Reid and Leslie Cuthbertson
Capsular polysaccharides (CPSs) and exopolysaccharides (EPSs) enhance bacterial survival in the environment, contribute to symbiotic interactions between plants and bacteria, and mediate interactions between plant and animal pathogens and their hosts. Bacteria express a wide array of CPS and EPS structures that are assembled by one of three distinct mechanisms. The Wzy-dependent polymerization system is characterized by the synthesis of lipid-linked repeat units in the cytoplasm, and their block-wise polymerization at the periplasmic face of the inner membrane. The resulting polymer is transported across the outer membrane (in Gram-negative organisms) via a channel formed by an outer membrane polysaccharide export (OPX) protein. The ATP-binding cassette (ABC) transporter-dependent system is defined by the synthesis of full-length CPS chains in the cytoplasm, their ABC transporter-dependent export across the inner membrane, and their subsequent transport across the outer membrane, presumably via a channel formed by an OPX protein. In the synthase-dependent system, a single enzyme achieves polymer initiation, synthesis and export across the membrane. This chapter describes these modes of CPS and EPS assembly, highlighting recent findings and identifying areas where further research is warranted.
3. Control of Lytic Transglycosylase Activity within Bacterial Cell Walls
John M. Pfeffer, Patrick J. Moynihan, Chelsea A. Clarke, Chris Vandenende and Anthony J. Clarke
Lytic transglycosylases are an important class of bacterial enzymes that act on peptidoglycan with the same substrate specificity as lysozyme. Unlike the latter enzymes however, the lytic transglycosylases are not hydrolases, but instead cleave the glycosidic linkage between N-acetylmuramyl and N-acetylglucosaminyl residues with the concomitant formation of a 1,6-anydromuramyl product. They are ubiquitous in bacteria which produce a complement of different forms that are responsible for creating space within the peptidoglycan sacculus for its biosynthesis and recycling, cell division, and the insertion of cell-envelope spanning structures, such as flagella and secretion systems. Given their catastrophic autolytic potential, the activity of lytic transglycosylases must be tightly controlled within the producing cells. Three modes of control at the enzymatic level have been identified: the modification of substrate, membrane association and complex formation, and the production of proteinaceous inhibitors. These modes of control and their potential as new targets for antibacterials are discussed.
4. Bacterial Flagellar Glycosylation Systems: Opportunities and Applications
Susan M. Twine and Susan M. Logan
The biosynthesis and assembly of the flagellar apparatus has been the subject of extensive studies over many decades. More recently, glycosylation of the major structural protein, the flagellin, has been shown to be an important component of numerous flagellar systems in both Archaea and Bacteria, playing either an integral role in assembly and for a number of bacterial pathogens a role in virulence. Increasingly, it is apparent that bacteria elaborate a structurally diverse array of flagellin-modifying glycans. This chapter focuses firstly upon reviewing recent research on the structural diversity in Gram-positive and Gram-negative flagellar glycosylation systems. In the second part, the ways in which flagellin glycosylation and associated biosynthetic pathways can be exploited are discussed.
5. Bacterial N-linked Glycosylation Systems: Current Knowledge and Future Perspectives
J. Cuccui, R.H. Langdon, M.G. Moule and Brendan W. Wren
Once thought to be restricted to eukaryotes and archaea, N-linked glycosylation has now been discovered in prokarytoes. Over the past decade, our understanding of bacterial N-linked glycosylations systems and their abundance has been expanding. This type of protein modification was first demonstrated in Campylobacter jejuni, a human gut pathogen, and we now know that N-linked glycosylation also exists in other ε-proteobacteria ranging from the deep-sea vent Nitratiruptor spp. and Sulfurovum spp. to sulfate reducing δ-proteobacteria. A greater understanding of these systems is necessary in order to comprehend the evolutionary reasons for their development and maintenance. In addition, this knowledge may also be exploited for glycoengineering purposes to produce cheaper subunit vaccines as well as humanized proteins.
6. Bacterial Lipoarabinomannan: Structure to Biogenesis
Arun K. Mishra, Sarah M. Batt, Luke J. Alderwick, Klaus Futterer, and Gurdyal Singh Besra
Lipoarabinomannan is an amphipathic lipoglycan found in the cell wall of most Actinomycetes. The majority of bacteria from the sub-order Corynebacterineae, including Mycobacterium tuberculosis, Mycobacterium smegmatis and Corynebacterium glutamicum, and from genus Rhodococcus, Gordonia and Amycolatopsis; all possess lipoarabinomannan and related glycoconjugates, such as lipomannan and phosphatidyl-myo-inositol mannosides. In addition to their physiological function in these microorganisms, these glycoconjugates play a key immunomodulatory role for pathogenic bacteria during infection. Herein, we report the work from this laboratory and several others, which has led to the biochemical characterization of key enzymes involved in the biogenesis of these complex glycoconjugates.
7. Protein Glycosylation in the Third Domain of Life: the Archaea
John F. Kelly and Ken F. Jarrell
Archaea are single-celled microorganisms that are sufficiently distinct as to constitute a third domain of life. It has been known for some time that Archaea express glycoproteins. However, research to understand the nature of their glycan modifications, the pathways used to produce them as well as their role in archaeal biology has lagged behind similar efforts in Eukarya and Bacteria, at least until recently. Here we describe in some detail the efforts made to determine the composition and structure of archaeal glycan posttranslational modifications and to elucidate their biosynthetic pathways.
8. Identification and Characterisation of Glycosylation in Bacterial Proteins
Nichollas E. Scott, Stuart J. Cordwell, John F. Kelly and Susan M. Twine
There are increasing numbers of reports of bacterial glycosylation in pathogenic bacteria, with well-characterized bacterial glycoproteins including pilins, flagellin and other surface-associated proteins. However, the discovery of bacterial glycoproteins can be challenging due to the diversity of glycans bacteria use to modify proteins. At the protein level, so-called 'top-down' mass spectrometry studies of intact protein can rapidly characterize bacterial glycan ions. At the peptide level, interpretation of individual bacterial glycopeptide tandem mass spectra can be challenging, owing to the diverse range of bacterial glycans produced. Reports of methods to specifically isolate bacterial glycopeptides are advancing knowledge of bacterial glycoproteomes. Herein, we provide an overview of protein and peptide centric mass spectrometry and related analytical techniques for the enrichment and analysis of bacterial glycoproteins.
9. Solid-state NMR of the Bacterial Cell Wall
Catherine Bougault, Sabine Hediger and Jean-Pierre Simorre
Liquid-state NMR is traditionally used to provide fine chemical and structural information on soluble fragments, but is limited to biomolecules in the fast rotational tumbling regime. On the other hand, solid-state NMR, unlimited by the molecular size, is extensively applied to polymers, but provides a spectral resolution that is hampered by orientational heterogeneity. This chapter analyzes the potential of high-resolution solid-state NMR in providing chemical, structural and dynamics information on whole bacteria or bacterial cell envelopes in lyophilized as well as in fully-hydrated samples. The first section addresses bacterial strain typing issues and discusses the choice of adequate nuclear probes, the concomitant requirements for efficient isotope labeling schemes and the NMR methods used to characterize the chemical composition of peptidoglycan, teichoic acids, lipopolysaccharides or mycolic acids in bacteria. The second section describes the principles used to characterize molecular interactions of proteins, ions, antibiotic/antimicrobial molecules with the bacterial cell wall by NMR. The third and last section gives an overview of the contribution of solid-state NMR to characterize the cell wall structure and dynamics, and covers the different techniques used to extract specific structural information as well as global mobility.
10. Methods for the Analysis of Microbial Lipid-Linked Oligosaccharides By Mass Spectrometry
Christopher W. Reid
Bacteria and Archaea produce a variety of glycoconjugates such as capsular polysaccharides, lipopolysaccharides, and glycoproteins that are assembled on a polyisoprenyl-phosphate lipid in the cytoplasmic membrane. Traditional methods to analyze the membrane-associated steps of glycan biosynthesis involved the use of metabolic radio-labeling or the indirect detection of lipid-associated glycans. Recent advances in analytical biochemistry now provide the microbial glycobiologist with a number of tools for the direct detection and characterization of low abundance lipid-linked oligosaccharides. Approaches include targeted glycolipidomics strategies, such as affinity-capture capillary electrophoresis mass spectrometry and global approaches such as separation on porous graphite carbon and normal phase liquid chromatography mass spectrometry (LC-MS). These techniques provide opportunities to probe the lipid-associated steps in glycan biosynthesis in greater detail as well as provide an enabling technology for the exploitation of these pathways in glycoengineering.
11. Synthesis of 4-acetamidohexoses in Bacteria: Structural Insights from the Bacillosamine and Nonulosonic Acid Pathways
Allan Matte, Ian C. Schoenhofen, Traian Sulea, Miroslaw Cygler and N. Martin Young
Many hexose sugars in bacteria undergo a variety of modifications, including oxidation/reduction, amination and acetylation, as part of biosynthesis into their final biologically-active forms. Enzymes that catalyze these reactions normally utilize nucleotide-linked sugar substrates, utilizing the nucleotide as an 'ancient handle' to bind and orient the sugar within the enzymes' active site. We and others have focused efforts on elucidating structure-function relationships for a subset of such biosynthetic enzymes, those associated with the synthesis of trideoxy-diacetamidohexoses, and the nonulsonate sugars subsequently derived from them. With structural information combined with site-directed mutagenesis, enzymatic analysis and molecular modeling, these studies have been essential to understanding the chemistry of how these enzymes bind their substrates and effect catalysis. Enzymes having different folds, such as N-acetyltransferases, can utilize different scaffolds to attain the same 4-acetamido-sugar product. In the case of dehydratases/epimerases and aminotransferases, the enzymes have a conserved structure, but utilize subtle differences within their active site to confer substrate binding and the nature of the final product. These studies depict the structural relationships between these enzymes, while at the same time high-lighting important differences that are beginning to reveal their function at the molecular level.
12. Application of Bacterial Glycosyltransferases in the Synthesis of Bioactive Glycans
It is now accepted that complex glycans play major roles in biology, such as the development of the embryo, the function of the immune system, microbial and viral pathogenesis and cellular communication, to name just a few. The many faceted roles that glycans play in biology makes them a challenge to understand on functional level, and the complexity of the structures themselves makes them daunting targets for chemical synthesis, which is required for examination of their binding interactions and for future development of carbohydrate based therapeutics. In order to facilitate the synthesis of complex glycans, we have been examining glycosyltransferases which make strategic linkages in biologically active glycans. Many of the mammalian enzymes have not been as easy to express as active recombinant proteins, and many have a more restricted acceptor specificity that limits their use for synthesis. Our focus has been on the use of bacterial enzymes from pathogens which make molecular mimics of host glycans, and which have been shown to be potent catalystsfor carbohydrate synthesis. This chapter will provide a review on a variety of bacterial enzymes that we and others have enabled for in vitro synthetic carbohydrate chemistry, as well as some promising in vivo production strategies for bioactive carbohydrates.
13. Metabolic Labeling of Bacterial Glycans with Chemical Reporters
Danielle H. Dube
Though long believed to be absent from bacteria, glycoproteins are now known to be synthesized in a number of bacterial species. Traditional methods to study glycoproteins have revealed fascinating glycan structures that are exclusively found in bacteria and are frequently linked to pathogenesis. In recent years, these methods have been augmented by a complementary approach, termed metabolic oligosaccharide engineering (MOE), to facilitate large scale systematic studies of the entire complement of glycan structures in bacteria, referred to as bacterial glycomics. In MOE, bacterial glycans are metabolically labeled with unique chemical functionalities, called chemical reporters. Labeling bacterial glycans in this manner facilitates glycoprotein detection and enrichment. In addition to enabling glycoprotein profiling, the labeled glycans can undergo selective covalent bond formation, thereby permitting further applications. For example, labeled glycans are poised to disrupt the bacterial surface coat, target bacterial cells with toxins, trap glycan-based host-pathogen interactions, and image dynamic changes in glycosylation. This chapter focuses on MOE methodology, its application to the study of bacterial glycoproteins, and its future role in treating infectious disease.
14. Glycoconjugate Vaccines
Abstract to follow
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(EAN: 9781904455950 Subjects: [microbiology] [bacteriology] [molecular microbiology] )