The glycome is the entire complement of sugars, whether free or present in more complex

molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...

s, of an

organism In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and ...

. An alternative definition is the entirety of

carbohydrate In organic chemistry, a carbohydrate () is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula (where ''m'' may or m ...

s in a

cell Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Locations * Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery ...

. The glycome may in fact be one of the most complex entities in

nature Nature, in the broadest sense, is the physical world or universe. "Nature" can refer to the phenomena of the physical world, and also to life in general. The study of nature is a large, if not the only, part of science. Although humans are ...

. "

Glycomics Glycomics is the comprehensive study of glycomes (the entire complement of sugars, whether free or present in more complex molecules of an organism), including genetic, physiologic, pathologic, and other aspects. Glycomics "is the systematic study ...

, analogous to genomics and proteomics, is the systematic study of all glycan structures of a given cell type or organism" and is a subset of

glycobiology Defined in the narrowest sense, glycobiology is the study of the structure, biosynthesis, and biology of saccharides ( sugar chains or glycans) that are widely distributed in nature. Sugars or saccharides are essential components of all living thin ...

. "

Carbohydrate In organic chemistry, a carbohydrate () is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula (where ''m'' may or m ...

", " glycan", "

saccharide In organic chemistry, a carbohydrate () is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula (where ''m'' may or ma ...

", and " sugar" are generic terms used interchangeably in this context and includes monosaccharides,

oligosaccharide An oligosaccharide (/ˌɑlɪgoʊˈsækəˌɹaɪd/; from the Greek ὀλίγος ''olígos'', "a few", and σάκχαρ ''sácchar'', "sugar") is a saccharide polymer containing a small number (typically two to ten) of monosaccharides (simple sug ...

s, polysaccharides, and derivatives of these compounds. Carbohydrates consist of “hydrated carbon”, i.e. H₂O. Monosaccharides are a carbohydrate that cannot be hydrolyzed into a simpler carbohydrate and are the building blocks of oligosaccharides and polysaccharides. Oligosaccharides are linear or branched chains of monosaccharides attached to one another via glycosidic linkages. The number of monosaccharide units can vary. Polysaccharides are glycans composed of repeating monosaccharides, generally greater than ten monosaccharide units in length. The glycome exceeds the complexity of the

proteome The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. ...

as a result of the even greater diversity of the glycome's constituent carbohydrates and is further complicated by the sheer multiplicity of possibilities in the combination and interaction of the carbohydrates with each other and with

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...

s. "The spectrum of all glycan structures — the glycome — is immense. In

human Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, cultu ...

s, its size is orders of magnitude greater than the number of proteins that are encoded by the genome, one percent of which encodes proteins that make, modify, localize or bind sugar chains, which are known as glycans." The outer surface of the cell is a sea of

lipids Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include ...

with a fleet of sugar molecules, many of which are attached to proteins, fats or both, that interact with molecules outside the cell and are critical for the communication between cells and the stickiness of a cell. "Glycans are nature's biologic modifiers," says Jamey Marth, a Howard Hughes Medical Institute investigator at the University of California San Diego."Glycans generally don't turn physiologic processes on and off, rather they modify the behavior of the cell by responding to external stimuli."

Tools used for research on glycome

The following are examples of the commonly used techniques in glycan analysis:

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-

glycans The terms glycans and polysaccharides are defined by IUPAC as synonyms meaning "compounds consisting of a large number of monosaccharides linked glycosidically". However, in practice the term glycan may also be used to refer to the carbohydrate ...

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. O-

are usually analysed without any tags, due to the chemical release conditions preventing them to be labeled. Fractionated glycans from

high-performance liquid chromatography High-performance liquid chromatography (HPLC), formerly referred to as high-pressure liquid chromatography, is a technique in analytical chemistry used to separate, identify, and quantify each component in a mixture. It relies on pumps to pa ...

(HPLC) instruments can be further analyzed by

MALDI In mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation. It has been applied to the analysis of b ...

-TOF-MS(MS) to get further information 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

-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 instead of

-MS, electrospray ionisation ( ESI) is more frequently used.

Multiple Reaction Monitoring (MRM)

Although MRM has been used extensively in metabolomics and proteomics, its high sensitivity and linear response over a wide dynamic range make it especially suited for glycan biomarker research and discovery. MRM is performed on a triple quadrupole (QqQ) instrument, which is set to detect a predetermined precursor ion in the first quadrupole, a fragmented in the collision quadrupole, and a predetermined fragment ion in the third quadrupole. It is a non-scanning technique, wherein each transition is detected individually and the detection of multiple transitions occurs concurrently in duty cycles. This technique is being used to characterize the immune glycome. Table 1:Advantages and disadvantages of mass spectrometry in glycan analysis

Arrays

Lectin and antibody arrays provide high-throughput screening of many samples containing glycans. This method uses either naturally occurring

lectins Lectins are carbohydrate-binding proteins that are highly specific for sugar groups that are part of other molecules, so cause agglutination of particular cells or precipitation of glycoconjugates and polysaccharides. Lectins have a role in rec ...

or artificial monoclonal antibodies, 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 The Consortium for Functional Glycomics (CFG) is a large research initiative funded in 2001 by a glue grant from the National Institute of General Medical Sciences (NIGMS) to “define paradigms by which protein-carbohydrate interactions mediate ...

an
Z Biotech LLC
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 azide-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 crystallography X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...

and

nuclear magnetic resonance (NMR) spectroscopy Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic fie ...

for complete structural analysis of complex glycans is a difficult and complex field. However, the structure of the binding site of numerous lectins,

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products ...

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 In chemical analysis, chromatography is a laboratory technique for the separation of a mixture into its components. The mixture is dissolved in a fluid solvent (gas or liquid) called the ''mobile phase'', which carries it through a system ( ...

(

affinity chromatography Affinity chromatography is a method of separating a biomolecule from a mixture, based on a highly specific macromolecular binding interaction between the biomolecule and another substance. The specific type of binding interaction depends on the ...

etc.) and analytical electrophoresis ( PAGE (polyacrylamide electrophoresis),

capillary electrophoresis Capillary electrophoresis (CE) is a family of electrokinetic separation methods performed in submillimeter diameter capillaries and in micro- and nanofluidic channels. Very often, CE refers to capillary zone electrophoresis (CZE), but other elect ...

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 elect ...

, etc.).

Sources and notes

External links

* {{Carbohydrates Glycomics

See also