Glycomics

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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.[1][2] Glycomics "is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology.[3] 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 genes) and proteomics (which deals with proteins).

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 (glycoprotein) 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 and RNA have four building blocks each (the nucleosides or nucleotides). Lipids are divided into eight categories based on ketoacyl and isoprene. Proteins have 20 (the amino acids). Saccharides have 32 types of sugar linkages.[4] 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 glycoproteins, but proteins specifically involved in binding and reacting with carbohydrate:

  • Carbohydrate-specific enzymes for synthesis, modulation, and degradation
  • Lectins, carbohydrate-binding proteins of all sorts
  • Receptors, circulating or membrane-bound carbohydrate-binding receptors

Importance

To answer this question one should know the different and important functions of glycans. The following are some of those functions:

There are important medical applications of aspects of glycomics:

Glycomics is particularly important in microbiology because glycans play diverse roles in bacterial physiology.[5] Research in bacterial glycomics could lead to the development of:

  • novel drugs
  • bioactive glycans
  • glycoconjugate vaccines

Tools used

The following are examples of the commonly used techniques in glycan analysis[3]

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.[6] In case of glycolipids, they can be analyzed directly without separation of the lipid component.

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).[7] 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.[8]

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.[9]

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)[10][11]


Table 1:Advantages and disadvantages of mass spectrometry in glycan analysis

Advantages Disadvantages
  • Applicable for small sample amounts (lower fmol range)
  • Useful for complex glycan mixtures (generation of a further analysis dimension).
  • Attachment sides can be analysed by tandem MS experiments (side specific glycan analysis).
  • Glycan sequencing by tandem MS experiments.
  • Destructive method.
  • Need of a proper experimental design.

Arrays

Lectin and antibody arrays provide high-throughput screening of many samples containing glycans. This method uses either naturally occurring lectins 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, 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 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 lectins, enzymes 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, capillary electrophoresis, affinity electrophoresis, etc.).

See also

References

  1. ^ Aoki-Kinoshita KF; Lewitter, Fran (May 2008). Lewitter, Fran (ed.). "An Introduction to Bioinformatics for Glycomics Research". PLoS Comput. Biol. 4 (5): e1000075. doi:10.1371/journal.pcbi.1000075. PMC 2398734. PMID 18516240.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  2. ^ Srivastava S (May 2008). "Move over proteomics, here comes glycomics". J. Proteome Res. 7 (5): 1799. doi:10.1021/pr083696k. PMID 18509903.
  3. ^ a b Essentials of Glycobiology (2nd ed.). Cold Spring Harbor Laboratory Press. 2009. ISBN 978-087969770-9.
  4. ^ ucsd news article Do 68 Molecules Hold the Key to Understanding Disease? published September 3, 2008
  5. ^ Reid, CW; Twine, SM; Reid, AN (editor) (2012). Bacterial Glycomics: Current Research, Technology and Applications. Caister Academic Press. ISBN 978-1-904455-95-0. {{cite book}}: |author= has generic name (help)CS1 maint: multiple names: authors list (link)
  6. ^ Wada Y, Azadi P, Costello CE; et al. (April 2007). "Comparison of the methods for profiling glycoprotein glycans—HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study". Glycobiology. 17 (4): 411–22. doi:10.1093/glycob/cwl086. PMID 17223647. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
  7. ^ Hase S, Ikenaka T, Matsushima Y (November 1978). "Structure analyses of oligosaccharides by tagging of the reducing end sugars with a fluorescent compound". Biochem. Biophys. Res. Commun. 85 (1): 257–63. doi:10.1016/S0006-291X(78)80037-0. PMID 743278.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  8. ^ Pabst M, Kolarich D, Pöltl G; et al. (January 2009). "Comparison of fluorescent labels for oligosaccharides and introduction of a new postlabeling purification method". Anal. Biochem. 384 (2): 263–73. doi:10.1016/j.ab.2008.09.041. PMID 18940176. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
  9. ^ Harvey DJ, Bateman RH, Bordoli RS, Tyldesley R (2000). "Ionisation and fragmentation of complex glycans with a quadrupole time-of-flight mass spectrometer fitted with a matrix-assisted laser desorption/ionisation ion source". Rapid Commun. Mass Spectrom. 14 (22): 2135–42. doi:10.1002/1097-0231(20001130)14:22<2135::AID-RCM143>3.0.CO;2-#. PMID 11114021.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  10. ^ Pabst M, Bondili JS, Stadlmann J, Mach L, Altmann F (July 2007). "Mass + retention time &#61; structure: a strategy for the analysis of N-glycans by carbon LC-ESI-MS and its application to fibrin N-glycans". Anal. Chem. 79 (13): 5051–7. doi:10.1021/ac070363i. PMID 17539604.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  11. ^ Ruhaak LR, Deelder AM, Wuhrer M (May 2009). "Oligosaccharide analysis by graphitized carbon liquid chromatography-mass spectrometry". Anal Bioanal Chem. 394 (1): 163–74. doi:10.1007/s00216-009-2664-5. PMID 19247642.{{cite journal}}: CS1 maint: multiple names: authors list (link)

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