Glycomics
Encyclopedia
Glycomics is the comprehensive study of glycomes (the entire complement of sugar
s, whether free or present in more complex molecule
s, of an organism
), including genetic, physiologic, pathologic, and other aspects. Glycomics "is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology
. The term glycomics is derived from the chemical prefix for sweetness or a sugar, "glyco-", and was formed to follow the naming convention established by genomics
(which deals with gene
s) and proteomics
(which deals with protein
s).
This area of research has to deal with an inherent level of complexity not seen in other areas of applied biology. 68 building blocks (molecules for DNA, RNA and proteins; categories for lipids; types of sugar linkages for saccharides) provide the structural basis for the molecular choreography that constitutes the entire life of a cell. DNA
and RNA
have four building blocks each (the nucleoside
s or nucleotide
s). Lipid
s are divided into eight categories based on ketoacyl and isoprene
. Protein
s have 20 (the amino acid
s). Saccharides have 32 types of sugar linkages. While these building blocks can be attached only linearly for proteins and genes, they can be arranged in a branched array for saccharides, further increasing the degree of complexity.
Add to this the complexity of the numerous proteins involved, not only as carriers of carbohydrate, the glycoprotein
s, but proteins specifically involved in binding and reacting with carbohydrate:
There are important medical applications of aspects of glycomics:
Glycomics is particularly important in microbiology because glycans play diverse roles in bacterial physiology. Research in bacterial glycomics could lead to the development of:
N and O-glycans
from glycoproteins are analyzed routinely by high-performance-liquid-chromatography (reversed phase, normal phase and ion exchange HPLC) after tagging the reducing end of the sugars with a fluorescent compound (reductive labeling).
A large variety of different labels were introduced in the recent years, where 2-aminobenzamide (AB), anthranilic acid (AA), 2-aminopyridin (PA), 2-aminoacridone (AMAC) and 3-(acetylamino)-6-aminoacridine (AA-Ac) are just a few of them.
Fractionated glycans from HPLC
instruments can be further analyzed by MALDI-TOF-MS(MS) to get further informations about structure and purity. Sometimes glycan pools are analyzed directly by mass spectrometry without prefractionation, although a discrimination between isobaric glycan structures is more challenging or even not always possible. Anyway, direct MALDI-TOF-MS analysis can lead to a fast and straightforward illustration of the glycan pool.
In recent years, high performance liquid chromatography online coupled to mass spectrometry became very popular. By choosing porous graphitic carbon as a stationary phase for liquid chromatography, even non derivatized glycans can be analyzed. Detection is here done by mass spectrometry, but in contrast to MALDI-MS with an electrospray ionisation (ESI
) interface(PGC-LC-ESI-MS or PGCC-MS)
Table 1:Advantages and disadvantages of mass spectrometry in glycan analysis
, where both are immobilized on a certain chip and incubated with a fluorescent glycoprotein sample.
Glycan arrays, like that offered by the Consortium for Functional Glycomics
, contain carbohydrate compounds that can be screened with lectins or antibodies to define carbohydrate specificity and identify ligands.
-labeled sugars which can be reacted using the Staudinger ligation. This method has been used for in vitro and in vivo imaging of glycans.
and nuclear magnetic resonance (NMR) spectroscopy
for complete structural analysis of complex glycans is a difficult and complex field. However, the structure of the binding site of numerous lectin
s, enzyme
s and other carbohydrate-binding proteins has revealed a wide variety of the structural basis for glycome function. The purity of test samples have been obtained through chromatography
(affinity chromatography
etc.) and analytical electrophoresis
(PAGE or polyacryl amide electrophoresis
, CE or capillary electrophoresis
, affinity electrophoresis
, etc.).
Sugar
Sugar is a class of edible crystalline carbohydrates, mainly sucrose, lactose, and fructose, characterized by a sweet flavor.Sucrose in its refined form primarily comes from sugar cane and sugar beet...
s, whether free or present in more complex molecule
Molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...
s, of an organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...
), including genetic, physiologic, pathologic, and other aspects. Glycomics "is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology
Glycobiology
Defined in the broadest sense, glycobiology is the study of the structure, biosynthesis, and biology of saccharides that are widely distributed in nature...
. The term glycomics is derived from the chemical prefix for sweetness or a sugar, "glyco-", and was formed to follow the naming convention established by genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
(which deals with gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s) and proteomics
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
(which deals with protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s).
Challenges
- The complexity of sugars: regarding their structures, they are not linear instead they are highly branched. Moreover, glycans can be modified (modified sugars), this increases its complexity.
- Complex biosynthetic pathways for glycans.
- Usually glycans are found either bound to protein (glycoproteinGlycoproteinGlycoproteins are proteins that contain oligosaccharide chains covalently attached to polypeptide side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known as glycosylation. In proteins that have segments extending...
) or conjugated with lipids (glycolipids). - Unlike genomes, glycans are highly dynamic.
This area of research has to deal with an inherent level of complexity not seen in other areas of applied biology. 68 building blocks (molecules for DNA, RNA and proteins; categories for lipids; types of sugar linkages for saccharides) provide the structural basis for the molecular choreography that constitutes the entire life of a cell. DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
and RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
have four building blocks each (the nucleoside
Nucleoside
Nucleosides are glycosylamines consisting of a nucleobase bound to a ribose or deoxyribose sugar via a beta-glycosidic linkage...
s or nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s). Lipid
Lipid
Lipids constitute a broad group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins , monoglycerides, diglycerides, triglycerides, phospholipids, and others...
s are divided into eight categories based on ketoacyl and isoprene
Isoprene
Isoprene , or 2-methyl-1,3-butadiene, is a common organic compound with the formula CH2=CCH=CH2. Under standard conditions it is a colorless liquid...
. Protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s have 20 (the amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
s). Saccharides have 32 types of sugar linkages. While these building blocks can be attached only linearly for proteins and genes, they can be arranged in a branched array for saccharides, further increasing the degree of complexity.
Add to this the complexity of the numerous proteins involved, not only as carriers of carbohydrate, the glycoprotein
Glycoprotein
Glycoproteins are proteins that contain oligosaccharide chains covalently attached to polypeptide side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known as glycosylation. In proteins that have segments extending...
s, but proteins specifically involved in binding and reacting with carbohydrate:
- Carbohydrate-specific enzymeEnzymeEnzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
s for synthesis, modulation, and degradation - LectinLectinLectins are sugar-binding proteins that are highly specific for their sugar moieties. They play a role in biological recognition phenomena involving cells and proteins. For example, some viruses use lectins to attach themselves to the cells of the host organism during infection...
s, carbohydrate-binding proteins of all sorts - Receptors, circulating or membrane-bound carbohydrate-binding receptors
Importance
To answer of this question one should know the different and important functions of glycans. The following are some of those functions:- GlycoproteinGlycoproteinGlycoproteins are proteins that contain oligosaccharide chains covalently attached to polypeptide side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known as glycosylation. In proteins that have segments extending...
s found on the cell surface play a critical role in bacterial and viral recognition. - They are involved in cellular signaling pathways and modulate cell function.
- They are important in innate immunity.
- They determine cancerCancerCancer , known medically as a malignant neoplasm, is a large group of different diseases, all involving unregulated cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumors, and invade nearby parts of the body. The cancer may also spread to more distant parts of the...
development. - They orchestrate the cellular fate, inhibit proliferationProliferationProliferation may refer to:*Nuclear proliferation*Chemical weapon proliferation*Cell proliferation* The proliferative phase of wound healing...
, regulate circulation and invasion. - They affect the stability and folding of proteinProteinProteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s. - They affect the pathway and fate of glycoproteinGlycoproteinGlycoproteins are proteins that contain oligosaccharide chains covalently attached to polypeptide side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known as glycosylation. In proteins that have segments extending...
s. - There are many glycan-specific diseases, often hereditary diseases.
There are important medical applications of aspects of glycomics:
- LectinLectinLectins are sugar-binding proteins that are highly specific for their sugar moieties. They play a role in biological recognition phenomena involving cells and proteins. For example, some viruses use lectins to attach themselves to the cells of the host organism during infection...
s fractionate cells to avoid graft-versus-host disease in stem cellStem cellThis article is about the cell type. For the medical therapy, see Stem Cell TreatmentsStem cells are biological cells found in all multicellular organisms, that can divide and differentiate into diverse specialized cell types and can self-renew to produce more stem cells...
transplantation. - Activation and expansion of cytolytic CD8CD8CD8 is a transmembrane glycoprotein that serves as a co-receptor for the T cell receptor . Like the TCR, CD8 binds to a major histocompatibility complex molecule, but is specific for the class I MHC protein. There are two isoforms of the protein, alpha and beta, each encoded by a different gene...
T cellT cellT cells or T lymphocytes belong to a group of white blood cells known as lymphocytes, and play a central role in cell-mediated immunity. They can be distinguished from other lymphocytes, such as B cells and natural killer cells , by the presence of a T cell receptor on the cell surface. They are...
s in cancer treatment.
Glycomics is particularly important in microbiology because glycans play diverse roles in bacterial physiology. Research in bacterial glycomics could lead to the development of:
- novel drugs
- bioactive glycans
- glycoconjugate vaccines
High Resolution Mass Spectrometry (MS) and High Performance Liquid Chromatography (HPLC)
The most commonly applied methods are MS and HPLC, in which the glycan part is cleaved either enzymatically or chemically from the target and subjected to analysis. In case of glycolipids, they can be analyzed directly without separation of the lipid component.N and O-glycans
Glycans
The term glycan refers to a polysaccharide or oligosaccharide. Glycans usually consist solely of O-glycosidic linkages of monosaccharides. For example, cellulose is a glycan composed of beta-1,4-linked D-glucose, and chitin is a glycan composed of beta-1,4-linked N-acetyl-D-glucosamine...
from glycoproteins are analyzed routinely by high-performance-liquid-chromatography (reversed phase, normal phase and ion exchange HPLC) after tagging the reducing end of the sugars with a fluorescent compound (reductive labeling).
A large variety of different labels were introduced in the recent years, where 2-aminobenzamide (AB), anthranilic acid (AA), 2-aminopyridin (PA), 2-aminoacridone (AMAC) and 3-(acetylamino)-6-aminoacridine (AA-Ac) are just a few of them.
Fractionated glycans from HPLC
High-performance liquid chromatography
High-performance liquid chromatography , HPLC, is a chromatographic technique that can separate a mixture of compounds and is used in biochemistry and analytical chemistry to identify, quantify and purify the individual components of the mixture.HPLC typically utilizes different types of stationary...
instruments can be further analyzed by MALDI-TOF-MS(MS) to get further informations about structure and purity. Sometimes glycan pools are analyzed directly by mass spectrometry without prefractionation, although a discrimination between isobaric glycan structures is more challenging or even not always possible. Anyway, direct MALDI-TOF-MS analysis can lead to a fast and straightforward illustration of the glycan pool.
In recent years, high performance liquid chromatography online coupled to mass spectrometry became very popular. By choosing porous graphitic carbon as a stationary phase for liquid chromatography, even non derivatized glycans can be analyzed. Detection is here done by mass spectrometry, but in contrast to MALDI-MS with an electrospray ionisation (ESI
ESI
- Companies and organizations :* Electro Scientific Industries , a high-technology company based in Oregon, United States* Employees’ State Insurance scheme, the national health and disability insurance for industry workers and other employees in India* Erwin Schrödinger Institute for Mathematical...
) interface(PGC-LC-ESI-MS or PGCC-MS)
Table 1:Advantages and disadvantages of mass spectrometry in glycan analysis
| Advantages | Disadvantages |
|---|---|
|
|
Arrays
Lectin and antibody arrays provide high-throughput screening of many samples containing glycans. This method uses either naturally occurring lectins or artificial monoclonal antibodiesMonoclonal antibodies
Monoclonal antibodies are monospecific antibodies that are the same because they are made by identical immune cells that are all clones of a unique parent cell....
, where both are immobilized on a certain chip and incubated with a fluorescent glycoprotein sample.
Glycan arrays, like that offered by the Consortium for Functional Glycomics
Consortium for Functional Glycomics
The Consortium for Functional Glycomics is a large research initiative funded in 2001 by a glue grant from the National Institute of General Medical Sciences to “define paradigms by which protein-carbohydrate interactions mediate cell communication”...
, contain carbohydrate compounds that can be screened with lectins or antibodies to define carbohydrate specificity and identify ligands.
Metabolic and covalent labeling of glycans
Metabolic labeling of glycans can be used as a way to detect glycan structures. A well known strategy involves the use of azideAzide
Azide is the anion with the formula N3−. It is the conjugate base of hydrazoic acid. N3− is a linear anion that is isoelectronic with CO2 and N2O. Per valence bond theory, azide can be described by several resonance structures, an important one being N−=N+=N−...
-labeled sugars which can be reacted using the Staudinger ligation. This method has been used for in vitro and in vivo imaging of glycans.
Tools for glycoproteins
X-ray crystallographyX-ray crystallography
X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...
and nuclear magnetic resonance (NMR) spectroscopy
Protein nuclear magnetic resonance spectroscopy
Nuclear magnetic resonance spectroscopy of proteins is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins. The field was pioneered by Richard R. Ernst and Kurt Wüthrich, among others...
for complete structural analysis of complex glycans is a difficult and complex field. However, the structure of the binding site of numerous lectin
Lectin
Lectins are sugar-binding proteins that are highly specific for their sugar moieties. They play a role in biological recognition phenomena involving cells and proteins. For example, some viruses use lectins to attach themselves to the cells of the host organism during infection...
s, enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
s and other carbohydrate-binding proteins has revealed a wide variety of the structural basis for glycome function. The purity of test samples have been obtained through chromatography
Chromatography
Chromatography is the collective term for a set of laboratory techniques for the separation of mixtures....
(affinity chromatography
Affinity chromatography
Affinity chromatography is a method of separating biochemical mixtures and based on a highly specific interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand.-Uses:Affinity chromatography can be used to:...
etc.) and analytical electrophoresis
Electrophoresis
Electrophoresis, also called cataphoresis, is the motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric field. This electrokinetic phenomenon was observed for the first time in 1807 by Reuss , who noticed that the application of a constant electric...
(PAGE or polyacryl amide electrophoresis
Page
-Position or occupation:* Page , a traditionally young male servant* Page * Page of Honour, a ceremonial position in the Royal Household of the Sovereign of the United Kingdom* A participant in any of the following programs:...
, CE or capillary electrophoresis
CE
CE, Ce or ce may refer to:* Common Era , secular alternative to Anno Domini * Cerium, chemical element with symbol Ce- Titles :* Chief Executive, administrative head of some regions...
, affinity electrophoresis
Affinity electrophoresis
Affinity electrophoresis is a general name for many analytical methods used in biochemistry and biotechnology. Both qualitative and quantitative information may be obtained through affinity electrophoresis. The methods include the so-called mobility shift electrophoresis, charge shift...
, etc.).
See also
- ProteomicsProteomicsProteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
- Omics
- List of omics topics in biology
- MetabolomicsMetabolomicsMetabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles...
- LipidomicsLipidomicsLipidomics may be defined as the large-scale study of pathways and networks of cellular lipids in biological systems The word "lipidome" is used to describe the complete lipid profile within a cell, tissue or organism and is a subset of the "metabolome" which also includes the three other major...
- CytomicsCytomicsCytomics is the study of cell systems at a single cell level. It combines all the bioinformatic knowledge to attempt to understand the molecular architecture and functionality of the cell system...
- InteractomicsInteractomicsInteractomics is a discipline at the intersection of bioinformatics and biology that deals with studying both the interactions and the consequences of those interactions between and among proteins, and other molecules within a cell. The network of all such interactions is called the Interactome...
- systems biologySystems biologySystems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...
- GlycomeDBGlycomeDBGlycomeDB is a database of carbohydrates including structural and taxonomic data....
External links
- List of Glycomics web sites
- Functional Glycomics Gateway, a collaboration between the Consortium for Functional GlycomicsConsortium for Functional GlycomicsThe Consortium for Functional Glycomics is a large research initiative funded in 2001 by a glue grant from the National Institute of General Medical Sciences to “define paradigms by which protein-carbohydrate interactions mediate cell communication”...
and Nature Publishing GroupNature Publishing GroupNature Publishing Group is an international publishing company that publishes academic journals, online databases, and services across the life, physical, chemical and applied sciences and clinical medicine... - glycosciences.de This site provides databases and bioinformatics tools for glycobiology and glycomics.
- GlycomeDB, A carbohydrate structure metadatabaseMetadatabaseMetadatabase is a database model for metadata management, global query of independent databases, and distributed data processing.This term is an addition to the dictionary. Originally, metadata is only a common term referring simply to "data about data", such as tags, keywords, and markup headers...
- EuroCarbDB
- ProGlycAn A short introduction to glycan analysis and a nomenclature for N-Glycans