Editing Glycome

{{Short description|Complete set of all sugars, free or bound, in an organism.}}
[[File:Glycome4TC.jpg|thumb|A glycome is composed of [[glycoprotein]]s and [[glycolipid]]s.]]

A '''glycome''' is the entire complement or complete set of all [[sugar]]s, whether free or chemically bound in more complex [[molecule]]s, of an [[organism]]. An alternative [[definition]] is the entirety of [[carbohydrate]]s in a [[cell (biology)|cell]]. The glycome may in fact be one of the most complex entities in [[nature]]. "[[Glycomics]], 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]].<ref>[http://www.cshlpress.com/default.tpl?action=full&--eqskudatarq=666 Cold Spring Harbor Laboratory Press] Essentials of Glycobiology, Second Edition</ref>

"[[Carbohydrate]]", "[[glycan]]", "[[saccharide]]", and "[[sugar]]" are generic terms used interchangeably in this context and includes [[monosaccharide]]s, [[oligosaccharide]]s, [[polysaccharide]]s, and derivatives of these compounds. Carbohydrates consist of "hydrated carbon", i.e. [CH<sub>2</sub>O]n. Monosaccharides are a carbohydrate that cannot be hydrolyzed into a simpler carbohydrate and are the building blocks of oligosaccharides and polysaccharides. [[Oligosaccharide]]s are linear or branched chains of monosaccharides attached to one another via glycosidic linkages. The number of monosaccharide units can vary. [[Polysaccharide]]s are glycans composed of repeating monosaccharides, generally greater than ten monosaccharide units in length.<ref>[https://web.archive.org/web/20040413212753/http://grtc.ucsd.edu/lecture1.pps Essentials of Glycobiology]</ref>

The glycome exceeds the complexity of the [[proteome]] 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]]s. "The spectrum of all [[glycan]] structures — the glycome — is immense. In [[human]]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."<ref>{{Cite journal |last=Freeze |first=Hudson H. |date=2006-07-01 |title=Genetic defects in the human glycome |url=https://www.nature.com/articles/nrg1894 |journal=Nature Reviews Genetics |language=en |volume=7 |issue=7 |pages=537–551 |doi=10.1038/nrg1894 |pmid=16755287 |issn=1471-0056|url-access=subscription }}</ref>

The outer surface of the cell is a sea of [[lipids]] 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."<ref>{{cite web|last=Trivedi |first=Bijal P. |url=http://www.genomenewsnetwork.org/articles/05_01/Glycome_project.shtml |url-status=dead |archive-date=May 25, 2022 |archive-url=https://web.archive.org/web/20220525215404/https://www.genomenewsnetwork.org/articles/05_01/Glycome_project.shtml |publisher=Genome News Network |title=The glycome project - A sugar-coated proposal |date=May 14, 2001}}</ref>

==Tools used for research on glycome==
The following are examples of the commonly used techniques in glycan analysis:<ref name="Cold Spring Harbor Laboratory Press">{{cite book |title=Essentials of Glycobiology |publisher=Cold Spring Harbor Laboratory Press |edition=2nd |year=2009 |isbn=9780879697709  |url=http://www.cshlpress.com/default.tpl?action=full&--eqskudatarq=666}}</ref>

===High-resolution mass spectrometry (MS) and high-performance liquid chromatography (HPLC)===
The most commonly applied methods are [[mass spectrometry|MS]] and [[high-performance liquid chromatography|HPLC]], in which the glycan part is cleaved either enzymatically or chemically from the target and subjected to analysis.<ref>{{cite journal  |vauthors=Wada Y, Azadi P, Costello CE, etal |title=Comparison of the methods for profiling glycoprotein glycans—HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study |journal=Glycobiology |volume=17 |issue=4 |pages=411–22 |date=April 2007 |pmid=17223647 |doi=10.1093/glycob/cwl086 |doi-access=free }}</ref> In case of glycolipids, they can be analyzed directly without separation of the lipid component.

N-[[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).<ref>{{cite journal |vauthors=Hase S, Ikenaka T, Matsushima Y |title=Structure analyses of oligosaccharides by tagging of the reducing end sugars with a fluorescent compound |journal=Biochem. Biophys. Res. Commun. |volume=85 |issue=1 |pages=257–63 |date=November 1978 |pmid=743278 |doi=10.1016/S0006-291X(78)80037-0}}</ref>
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.<ref>{{cite journal  |vauthors=Pabst M, Kolarich D, Pöltl G, etal |title=Comparison of fluorescent labels for oligosaccharides and introduction of a new postlabeling purification method |journal=Anal. Biochem. |volume=384 |issue=2 |pages=263–73 |date=January 2009 |pmid=18940176 |doi=10.1016/j.ab.2008.09.041 }}</ref>

O-[[glycans]] are usually analysed without any tags, due to the chemical release conditions preventing them to be labeled.

Fractionated glycans from [[high-performance liquid chromatography]] (HPLC) instruments can be further analyzed by [[MALDI]]-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 [[MALDI]]-TOF-MS analysis can lead to a fast and straightforward illustration of the glycan pool.<ref>{{cite journal |vauthors=Harvey DJ, Bateman RH, Bordoli RS, Tyldesley R |title=Ionisation and fragmentation of complex glycans with a quadrupole time-of-flight mass spectrometer fitted with a matrix-assisted laser desorption/ionisation ion source |journal=Rapid Commun. Mass Spectrom. |volume=14 |issue=22 |pages=2135–42 |year=2000 |pmid=11114021 |doi=10.1002/1097-0231(20001130)14:22<2135::AID-RCM143>3.0.CO;2-# |bibcode=2000RCMS...14.2135H }}</ref>

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 [[MALDI]]-MS, electrospray ionisation ([[Electrospray ionization|ESI]]) is more frequently used.<ref>{{cite journal|last1=Schulz|first1=BL|last2=Packer NH|first2=NH|last3=Karlsson|first3=NG|title=Small-scale analysis of O-linked oligosaccharides from glycoproteins and mucins separated by gel electrophoresis.|journal=Anal. Chem.|volume=74|issue=23|pages=6088–97|pmid=12498206|doi=10.1021/ac025890a|date=Dec 2002}}</ref><ref>{{cite journal |vauthors=Pabst M, Bondili JS, Stadlmann J, Mach L, Altmann F |title=Mass + retention time <nowiki>=</nowiki> structure: a strategy for the analysis of N-glycans by carbon LC-ESI-MS and its application to fibrin N-glycans |journal=Anal. Chem. |volume=79 |issue=13 |pages=5051–7 |date=July 2007 |pmid=17539604 |doi=10.1021/ac070363i }}</ref><ref>{{cite journal |vauthors=Ruhaak LR, Deelder AM, Wuhrer M |title=Oligosaccharide analysis by graphitized carbon liquid chromatography-mass spectrometry |journal=Anal Bioanal Chem |volume=394 |issue=1 |pages=163–74 |date=May 2009 |pmid=19247642 |doi=10.1007/s00216-009-2664-5 |doi-access=free }}</ref>

===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.<ref name="immune_glycan">{{cite journal |vauthors=Maverakis E, Kim K, Shimoda M, Gershwin M, Patel F, Wilken R, Raychaudhuri S, Ruhaak LR, Lebrilla CB | title = Glycans in the immune system and The Altered Glycan Theory of Autoimmunity | journal = J Autoimmun | volume = 57 | issue = 6 | pages = 1–13 | year = 2015 | pmid = 25578468 | doi = 10.1016/j.jaut.2014.12.002 | pmc=4340844}}</ref><ref>{{Cite journal|last1=Flowers|first1=Sarah A.|last2=Ali|first2=Liaqat|last3=Lane|first3=Catherine S.|last4=Olin|first4=Magnus|last5=Karlsson|first5=Niclas G.|date=2013-04-01|title=Selected reaction monitoring to differentiate and relatively quantitate isomers of sulfated and unsulfated core 1 O-glycans from salivary MUC7 protein in rheumatoid arthritis|journal=Molecular & Cellular Proteomics|volume=12|issue=4|pages=921–931|doi=10.1074/mcp.M113.028878|doi-access=free |issn=1535-9484|pmc=3617339|pmid=23457413}}</ref>

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

{| class="wikitable" border="1"
|-
! '''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]] and [http://www.zbiotech.com/ 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]] and [[Protein nuclear magnetic resonance spectroscopy|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|PAGE (polyacrylamide electrophoresis)]], [[capillary electrophoresis]], [[affinity electrophoresis]], etc.).

==See also==
*[[Glycomics]]
*[[Cell adhesion]]
*[[Glycolipid]]
*[[Glycoprotein]]
*[[List of omics topics in biology]]

==Sources and notes==
<references/>

==Further reading==
*[http://www.bio-itworld.com/ ''Bio-IT World''] a periodical covering glycomics
*{{cite journal |vauthors=Hirabayashi J, Arata Y, Kasai K |title=Glycome project: concept, strategy and preliminary application to ''Caenorhabditis elegans'' |journal=Proteomics |volume=1 |issue=2 |pages=295–303 |date=February 2001 |pmid=11680876 |doi=10.1002/1615-9861(200102)1:2<295::AID-PROT295>3.0.CO;2-C |s2cid=42203562 }} (A proposal to base the glycome project on ''[[Caenorhabditis elegans]]'', a microscopic worm, whose entire genome is already sequenced)
*[https://web.archive.org/web/20140517123416/http://glycochip.com/ 'GlycoChip']
*[https://www.ibiology.org/biochemistry/glycans/ Carolyn Bertozzi's Seminar: "Chemical Glycobiology"]

==External links==
*{{Cite web|title=The Human Glycome Project|url=https://human-glycome.org/}}

{{Carbohydrates}}

[[Category:Glycomics]]