Team:Exeter/Results/GlycoBase

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<p>By searching different databases online we were able to catalogue over 120 glycosyltransferases from different strains of <i>E. coli</i>. We set up the database so that the enzymes could be categorised by their acceptor and donor sugars. From that we were able to determine which sugars we would be able to stick together with the particular glycosyltransferases that we found. We called this database GlycoBase and this was the foundation of our project.</p>
 
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    <p>GlycoBase</p>
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    <p>GlycoBase is absolutely critical to our project. This database, that we have curated, currently has in excess of 150 glycosyltransferases entries (or GTases for short)
 +
    which contains information on the enzyme name, sugar donor, sugar acceptor, bond linkage, origin of GTase and how well characterised the enzyme may be. For example, an entry
 +
    could be: WbnK, alpha-D-GlcNAc, beta-D-Galactose, alpha-D-GlcNAc-(1->4)-beta-D-Galactose, Escherichia coli, YES. The user interface, GlycoWeb, interrogates GlycoBase to
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    deliver the appropriate GTases that will build the specific bespoke polysaccharide that the user intends to be produced.</p>
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    <br>
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    <p>In the future, we hope that by using the modelling (please link to modelling) aspects created for our project, we can include optimisation into GlycoBase. This would
 +
    improve polysaccharide yields and efficiencies, speed of turnover and even control selectivity of GTases to tailor production of polysaccharides even more to the user’s
 +
    specifications.</p>
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    <br>
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    <p>We drew the majority of our GTases from the Escherichia coli O-antigen Database (ECODAB)<sup>1</sup> that was created by Stockholm University to give a comprehensive list
 +
    of glycosylation reactions as well as the enzymes responsible for these reactions. Whilst this was a great starting point for adding GTases to our database GlycoBase, we hope
 +
    beyond this summer that anyone is able to add new entries into the database to increase the scope of GTases from organisms than simply Escherichia coli. For example, sucrose
 +
    synthase could be added to GlycoBase whose origin is from Arabidopsis thaliana instead, or more elaborate examples such as GmhD from Campylobacter jejuni. The ultimate
 +
    ambition of GlycoBase is to have a wide variety of different GTases, performing different glycosylation reactions from different species entirely, to produce any bespoke
 +
    polysaccharide that the user may like to be manufactured.</p>
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    <br>
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    <br>
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    <p><sup>1</sup> <i>Lundborg M., Modhukur V., Widmalm G. (2009) Glycosyltransferase Functions of E. coli O-antigens. Glycobiology. 20:366-368.</i></p>
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     <td>Beta-L-Rha</td>
     <td>Beta-L-Rha</td>
     <td>Beta-L-Rha</td>
     <td>Beta-L-Rha</td>

Revision as of 22:25, 26 September 2012


Glycobase

GlycoBase

GlycoBase is absolutely critical to our project. This database, that we have curated, currently has in excess of 150 glycosyltransferases entries (or GTases for short) which contains information on the enzyme name, sugar donor, sugar acceptor, bond linkage, origin of GTase and how well characterised the enzyme may be. For example, an entry could be: WbnK, alpha-D-GlcNAc, beta-D-Galactose, alpha-D-GlcNAc-(1->4)-beta-D-Galactose, Escherichia coli, YES. The user interface, GlycoWeb, interrogates GlycoBase to deliver the appropriate GTases that will build the specific bespoke polysaccharide that the user intends to be produced.


In the future, we hope that by using the modelling (please link to modelling) aspects created for our project, we can include optimisation into GlycoBase. This would improve polysaccharide yields and efficiencies, speed of turnover and even control selectivity of GTases to tailor production of polysaccharides even more to the user’s specifications.


We drew the majority of our GTases from the Escherichia coli O-antigen Database (ECODAB)1 that was created by Stockholm University to give a comprehensive list of glycosylation reactions as well as the enzymes responsible for these reactions. Whilst this was a great starting point for adding GTases to our database GlycoBase, we hope beyond this summer that anyone is able to add new entries into the database to increase the scope of GTases from organisms than simply Escherichia coli. For example, sucrose synthase could be added to GlycoBase whose origin is from Arabidopsis thaliana instead, or more elaborate examples such as GmhD from Campylobacter jejuni. The ultimate ambition of GlycoBase is to have a wide variety of different GTases, performing different glycosylation reactions from different species entirely, to produce any bespoke polysaccharide that the user may like to be manufactured.



1 Lundborg M., Modhukur V., Widmalm G. (2009) Glycosyltransferase Functions of E. coli O-antigens. Glycobiology. 20:366-368.
Donor
Acceptor
Bonding
Organism
Branching
Characterised
D-GalNAc Und-P Und-P-P-GlcNAc Escherichia coli
N
NO
D-GalNAc Und-P Und-P-P-GlcNAc Escherichia coli
N
NO
D-GalNAc Und-P Und-P-P-GlcNAc Escherichia coli
N
NO
Alpha-D-Gal Beta-D-GalNAc Alpha-D-Gal(1->3)-Beta-D-GalNAc Escherichia coli
N
YES
Alpha-D-Gal Alpha-L-Fuc Alpha-D-Gal-(1->3)-(Alpha-L-Fuc-(1->2))-Beta-D-Gal Escherichia coli
N
NO
Alpha-D-Gal Alpha-L-FucNAm Alpha-D-Gal-(1->3)-Alpha-L-FucNAm Escherichia coli
N
NO
Beta-D-Gal Beta-D-GalNAc Beta-D-Gal(1->3)-Beta-D-GalNAc Escherichia coli
N
NO
Beta-D-Gal Alpha-D-GalNAc Beta-D-Gal-(1->3)-Alpha-D-GalNAc Escherichia coli
N
NO
Beta-D-Gal Beta-D-Gal Beta-D-Gal-(1->4)-Beta-D-Gal Escherichia coli
Y
NO
Beta-D-Gal Beta-D-Glc Beta-D-Gal-(1->4)-Beta-D-Glc Escherichia coli
N
NO
Beta-D-Gal Beta-D-Galf Beta-D-Gal-(1->6)-Beta-D-Galf Escherichia coli
N
NO
Alpha-D-GalA Alpha-L-Fuc Alpha-D-GalA-(1->3)-Alpha-L-Fuc Shigella dysenteriae
N
NO
Beta-D-GalA Alpha-D-GlcNAc Beta-D-GalA-(1->3)-Alpha-D-GlcNAc Shigella boydii
N
NO
Alpha-D-GalNAc Alpha-D-GalNAc Alpha-D-GalNAc-(1->3)-Alpha-D-GalNAc Escherichia coli
N
NO
Beta-D-GalNAc Alpha-D-Gal Beta-D-GalNAc(1->4)-Alpha-D-Gal Escherichia coli
N
YES
Alpha-L-Fuc Beta-D-Gal Alpha-L-Fuc-(1->2)-Beta-D-Gal Escherichia coli
Y
YES
Alpha-L-FucNAc Alpha-D-Glc Alpha-L-FucNAc-(1->4)-Alpha-D-Glc Escherichia coli
N
NO
Alpha-L-FucNAc Alpha-D-GlcNAc Alpha-L-FucNAc-(1->3)-Alpha-D-GlcNAc Escherichia coli
N
NO
Alpha-L-FucNAm Beta-D-GlcNAc Alpha-L-FucNAm-(1->3)-Beta-D-GlcNAc Escherichia coli
N
NO
Alpha-L-Rha Alpha-L-Rha Alpha-L-Rha-(1->3)-Alpha-L-Rha Escherichia coli
N
NO
Alpha-L-Rha Alpha-L-Rha Alpha-L-Rha-(1->2)-Alpha-L-Rha  Escherichia coli
N
NO
Alpha-L-Rha Alpha-D-Glc Alpha-L-Rha-(1->6)-Alpha-D-Glc Escherichia coli
N
NO
Alpha-L-Rha Alpha-D-Man Alpha-L-Rha-(1->3)-Alpha-D-Man Escherichia coli
Y
NO
Alpha-L-Rha Beta-L-Rha Alpha-L-Rha-(1->3)-Alpha-D-GlcNAc Escherichia coli
N
NO
Alpha-L-Rha Alpha-L-Rha Alpha-L-Rha-(1->3)-Alpha-D-GlcNAc Escherichia coli
N
NO
Alpha-L-Rha Alpha-D-GlcNAc Alpha-L-Rha-(1->3)-Alpha-D-GlcNAc Escherichia coli
N
NO
Alpha-L-Rha Alpha-L-FucNAc Alpha-L-Rha-(1->4)-Alpha-L-FucNAc Escherichia coli
N
NO
Beta-L-Rha Beta-D-GlcNAc Beta-L-Rha-(1->3)-Beta-D-GlcNAc Escherichia coli
N
NO
Beta-L-Rha Beta-L-Rha Beta-L-Rha-(1->4)-Beta-L-Rha Escherichia coli
N
NO
Beta-L-Rha Beta-D-GlcNAc Beta-L-Rha-(1->4)-Beta-D-GlcNAc Escherichia coli
N
NO
Beta-L-Rha Alpha-D-GlcNAc Beta-L-Rha-(1->4)-Alpha-D-GlcNAc Escherichia coli
Y
NO
Alpha-D-Man Beta-D-GlcNAc Alpha-D-Man-(1->3)-Beta-D-GlcNAc Escherichia coli
N
NO
Alpha-D-Man Alpha-D-Man Alpha-D-Man-(1->3)-Alpha-D-Man Escherichia coli
N
NO
Alpha-D-Man Beta-D-Gal Alpha-D-Man-(1->4)-Beta-D-Gal Escherichia coli
N
NO
Alpha-D-Man Alpha-D-Man Alpha-D-Man-(1->2)-Alpha-D-Man Escherichia coli
N
NO
Beta-D-Man Alpha-D-GlcNAc Beta-D-Man-(1->3)-Alpha-D-GlcNAc Escherichia coli
N
NO
Beta-D-Man Beta-D-Gal Beta-D-Man-(1->3)-Beta-D-Gal Escherichia coli
N
NO
Alpha-D-Galf Beta-D-GalA Alpha-D-Galf-(1->4)-Beta-D-GalA Shigella boydii
Y
NO
Beta-D-Galf Alpha-D-Glc Beta-D-Galf-(1->6)-Alpha-D-Glc Escherichia coli
N
NO
Beta-D-Galf Beta-D-Galf Beta-D-Galf-(1->5)-Beta-D-Galf Shigella boydii
N
NO
Beta-D-Galf Beta-D-GlcNAc Beta-D-Galf-(1->3)-Beta-D-GlcNAc Shigella boydii
N
NO
Beta-D-Galf Beta-D-GlcNAc Beta-D-Galf-(1->3)-Beta-D-GlcNAc Shigella boydii
N
NO
Beta-D-Galf Beta-D-GalNAc Beta-D-Galf-(1->3)-Beta-D-GalNAc Escherichia coli
N
NO
Alpha-D-Glc Alpha-D-Glc Alpha-D-Glc-(1->4)-Alpha-D-Glc Escherichia coli
N
NO
Alpha-D-Glc Alpha-L-Rha Alpha-D-Glc-(1->3)-Alpha-L-Rha Escherichia coli
N
NO
Alpha-D-Glc Alpha-L-FucNAc Alpha-D-Glc-(1->3)-Alpha-L-FucNAc Escherichia coli
N
NO
Alpha-D-Glc Beta-D-Glc Alpha-D-Glc-(1->2)-Beta-D-Glc Escherichia coli
N
NO
Alpha-D-Glc Alpha-D-Glu Alpha-D-Glc-(1->4)-Alpha-D-Glc-(1->4)-1,4-Alpha-D-Glu Escherichia coli
N
NO
Beta-D-Glc Beta-D-GalNAc Beta-D-Glc-(1->3)-Beta-D-GalNAc Escherichia coli
N
NO
Beta-D-Glc Alpha-D-GalNAc Beta-D-Glc-(1->3)-Alpha-D-GalNAc Escherichia coli
N
NO
Beta-D-Glc Beta-D-GlcNAc Beta-D-Glc-(1->3)-Beta-D-GlcNAc Escherichia coli
N
NO
Beta-D-GlcA Alpha-D-GlcNAc Beta-D-GlcA-(1->4)-Alpha-D-GlcNAc Escherichia coli
N
NO
Beta-D-GlcA Alpha-D-Man Beta-D-GlcA-(1->2)-Alpha-D-Man Escherichia coli
N
NO
Alpha-D-GlcNAc Und-P Alpha-D-GlcNAc-P-P-Und Escherichia coli
N
NO
Alpha-D-GlcNAc Beta-D-Galf Alpha-D-GlcNAc-(1->2)-Beta-D-Galf Shigella boydii
N
NO
Alpha-D-GlcNAc Alpha-D-GalA Beta-D-GlcNAc-(1->4)-Alpha-D-GalA Shigella dysenteriae
N
NO
Alpha-D-GlcNAc Alpha-D-GlcA Alpha-D-GlcNAc-(1->4)-Alpha-DGlcA Escherichia coli
N
NO
Alpha-D-GlcNAc Alpha-D-Glc Alpha-D-GlcNAc-(1->6)-Alpha-D-Glc Escherichia coli
N
NO
Alpha-D-GlcNAc Beta-D-GlcNAc Alpha-D-GlcNAc-(1->3)-Beta-D-GlcNAc Escherichia coli
N
NO
Beta-D-GlcNAc Alpha-L-Rha Beta-D-GlcNAc-(1->2)-Alpha-L-Rha Escherichia coli
N
NO
Beta-D-GlcNAc Beta-D-Glc Beta-D-GlcNAc-(1->2)-Beta-D-Glc Escherichia coli
Y
NO
Alpha-Neu5Ac Beta-D-GlcNAc Alpha-Neu5Ac-(2->6)-Beta-D-Gal-(1->4)-Beta-D-GlcNAc Drosophila spp.
N
NO
Beta-D-Glc Beta-D-GlcNAc Beta-D-Glc-(1->3)-Beta-D-GlcNAc Escherichia coli
N
NO
Alpha-D-Gal Beta-D-Glc Alpha-D-Gal-(1->2)-Beta-D-Glc Escherichia coli
Y
NO
Alpha-Neu5Ac Beta-D-Glc Alpha-Neu5Ac-(2->3)-Beta-D-Glc Escherichia coli
N
NO
Alpha-D-Gal Beta-D-GlcNAc Alpha-D-Gal-(1->3)-Beta-D-GlcNAc Escherichia coli
N
NO
Beta-D-Gal Beta-D-GlcNAc Beta-D-Gal-(1->3)-Beta-D-GlcNAc Escherichia coli
Y
NO
Beta-D-GlcNAc Alpha-D-Gal Beta-D-GlcNAc-(1->3)-Alpha-D-Gal Escherichia coli
N
NO
Alpha-L-6dTal Alpha-D-FucNAc Alpha-L-6dTal-(1->3)-Alpha-D-FucNAc Escherichia coli
N
NO
Beta-D-Glc Alpha-L-6dTal Beta-D-Glc-(1->3)-Alpha-L-6dTal Escherichia coli
N
NO
Alpha-D-Gal Beta-D-GlcNAc Alpha-D-Gal-(1->3)-Beta-D-GlcNAc Escherichia coli
N
NO
Beta-D-Gal Beta-D-Man Beta-D-Gal-(1->4)-Beta-D-Man Escherichia coli
N
NO
Beta-D-Man Alpha-D-Gal Beta-D-Man-(1->4)-Alpha-D-Gal Escherichia coli
N
NO
Alpha-D-Glc Alpha-D-Gal Alpha-D-Glc-(1->6)-Alpha-D-Gal Shigella dysenteriae
N
NO
Alpha-D-Gal Alpha-L-FucNAc Alpha-D-Gal-(1->3)-Alpha-L-FucNAc Shigella dysenteriae
Y
NO
Beta-D-Glc Alpha-L-FucNAc Beta-D-Glc-(1->4)-Alpha-L-FucNAc Shigella dysenteriae
N
NO
Beta-D-GlcNAc Beta-D-Galf Beta-D-GlcNAc-(1->3)-Beta-D-Galf Escherichia coli
N
NO
Beta-D-Galf Alpha-D-GlcNAc Beta-D-Galf-(1->3)-Alpha-D-GlcNAc Escherichia coli
N
NO
Alpha-D-Man Alpha-D-Man Alpha-D-Man-(1->4)-Alpha-D-Man Escherichia coli
N
NO
Alpha-D-Man Beta-D-GlcNAc Alpha-D-Man-(1->3)-Beta-D-GlcNAc Escherichia coli
N
NO
Alpha-D-GlcNAc Beta-D-Man Alpha-D-GlcNAc-(1->2)-Beta-D-Man Escherichia coli
N
NO
Beta-D-Glc Alpha-L-6dTal Beta-D-Glc-(1->3)-Alpha-L-6dTal Escherichia coli
N
NO
Alpha-D-Man Beta-D-Man Alpha-D-Man-(1->2)-Beta-D-Man Escherichia coli
N
NO
Alpha-D-Man Alpha-D-Man Alpha-D-Man-(1->2)-Alpha-D-Man Escherichia coli
N
NO
Beta-D-Man Alpha-D-GlcNAc Beta-D-Man-(1->3)-Alpha-D-GlcNAc Escherichia coli
N
NO
Alpha-D-Gal Beta-D-Gal Alpha-D-Gal-(1->3)-Beta-D-Gal Escherichia coli
Y
NO
Beta-D-Gal Alpha-D-GalNAc Beta-D-Gal-(1->3)-Alpha-D-GalNAc Escherichia coli
N
NO
Beta-D-Gal Beta-D-GalNAc Beta-D-Gal-(1->3)-Beta-D-GalNAc Escherichia coli
N
NO
Alpha-D-GalNAc Beta-D-GalNAc Alpha-D-GalNAc-(1->3)-Beta-D-GalNAc Escherichia coli
N
NO
Beta-D-Gal Beta-D-GlcNAc Beta-D-Gal-(1->4)-Beta-D-GlcNAc Escherichia coli
N
NO
Alpha-L-QuiNAc Alpha-D-GalNAcA Alpha-L-QuiNAc-(1->4)-Alpha-D-GalNAcA Escherichia coli
N
NO
Alpha-D-GalNAcA Alpha-L-QuiNAc Alpha-D-GalNAcA-(1->3)-Alpha-L-QuiNAc Escherichia coli
N
NO
Alpha-L-QuiNAc Beta-D-GlcNAc Alpha-L-QuiNAc-(1->3)-Beta-D-GlcNAc Escherichia coli
N
NO
Alpha-D-Rha Alpha-D-Rha Alpha-D-Rha-(1->2)-Alpha-D-Rha Escherichia coli
N
NO
Alpha-D-Rha Alpha-D-Rha Alpha-D-Rha-(1->3)-Alpha-D-Rha Escherichia coli
N
NO
Alpha-Neu5Ac Beta-D-Gal Alpha-D-Neu5Ac-(2->3)-Beta-D-Gal Escherichia coli
N
NO
Alpha-D-Gal Alpha-Neu5Ac Alpha-D-Gal-(1->4)-Alpha-Neu5Ac Escherichia coli
N
NO
Beta-D-Gal Beta-D-GalNAc Beta-D-Gal-(1->3)-Beta-D-GalNAc Escherichia coli
N
NO
Beta-D-Ribf Alpha-L-Rha Beta-D-Ribf-(1->2)-Alpha-L-Rha Escherichia coli
Y
NO
Beta-D-GalNAc Alpha-L-Rha Beta-D-GalNAc-(1->3)-Alpha-L-Rha Escherichia coli
N
NO
Alpha-L-Rha Alpha-D-GlcNAc Alpha-L-Rha-(1->4)-Alpha-D-GlcNAc Escherichia coli
N
NO
Alpha-D-GlcNAc Beta-D-Gal Alpha-D-GlcNAc-(1->4)-Beta-D-Gal Escherichia coli
N
NO
Beta-D-Gal Alpha-D-GalNAc Beta-D-Gal-(1->3)-Alpha-D-GalNAc Escherichia coli
N
NO
Alpha-D-Gal Beta-D-GlcNAc Alpha-D-Gal-(1->3)-Beta-D-GlcNAc Escherichia coli
N
NO
Alpha-Col Alpha-D-Glc Alpha-Col-(1->3)-Alpha-D-Glc OR Alpha-Col-(1->6)-Alpha-D-Glc Escherichia coli
Y
NO
Beta-D-GlcNAc Alpha-D-GalNAc Beta-D-GlcNAc-(1->3)-Alpha-D-GalNAc Escherichia coli
Y
NO
Alpha-D-GalNAc Alpha-D-Glc Alpha-D-GalNAc-(1->4)-Alpha-D-Glc Shigella boydii
N
NO
Beta-D-Gal Alpha-D-GalNAc Beta-D-Gal-(1->3)-Alpha-D-GalNAc Escherichia coli
Y
NO
Alpha-D-GalA Alpha-D-Gal Alpha-D-GalA-(1->3)-Alpha-D-Gal Escherichia coli
N
NO
Alpha-D-GalNAc Alpha-D-GalA Alpha-D-GalNAc-(1->4)-Alpha-D-GalA Escherichia coli
N
NO
Alpha-D-Gal Beta-D-GlcNAc Alpha-D-Gal-(1->3)-Beta-D-GlcNAc Escherichia coli
N
NO
Beta-D-Ribf Beta-D-Gal Beta-D-Ribf-(1->4)-Beta-D-Gal Escherichia coli
N
NO
Beta-D-Gal Alpha-D-GlcNAc Beta-D-Gal-(1->3)-Alpha-D-GlcNAc Escherichia coli
N
NO
Beta-D-GalNAc Alpha-L-Rha Beta-D-GalNAc-(1->3)-Alpha-L-Rha Escherichia coli
N
NO
Alpha-L-Rha Alpha-D-Glc Alpha-L-Rha-(1->4)-Alpha-D-Glc Escherichia coli
N
NO
Alpha-D-Glc Beta-D-Gal Alpha-D-Glc-(1->4)-Beta-D-Gal Escherichia coli
N
NO
Beta-D-Gal Alpha-D-GalNAc Beta-D-Gal-(1->3)-Alpha-D-GalNAc Escherichia coli
N
NO
Alpha-D-Glc Alpha-D-Gal Alpha-D-Glc-(1->2)-Alpha-D-Gal Escherichia coli
N
NO
Alpha-D-Glc Alpha-D-Glc Alpha-D-Glc-(1->2)-Alpha-D-Glc Escherichia coli
N
NO
Alpha-D-Gal Alpha-D-Glc Alpha-D-Gal-(1->2)-Alpha-D-Glc Escherichia coli
N
NO
Alpha-D-Glc Alpha-D-Glc Alpha-D-Glc-(1->3)-Alpha-D-Glc Escherichia coli
N
NO
Alpha-D-Gal Alpha-D-Gal Alpha-D-Gal-(1->2)-Alpha-D-Gal Escherichia coli
Y
NO
Beta-D-Glc Alpha-D-Glc Beta-D-Glc-(1->3)-Alpha-D-Glc Escherichia coli
Y
NO
Alpha-D-Gal Alpha-D-Glc Alpha-D-Gal-(1->6)-Alpha-D-Glc Escherichia coli
Y
NO
Alpha-D-GlcNAc Alpha-D-Glc Alpha-D-GlcNAc-(1->2)-Alpha-D-Glc Escherichia coli
Y
NO
Alpha-D-Glc Alpha-D-Glc Alpha-D-Glc-(1->2)-Alpha-D-Glc Escherichia coli
Y
NO
Alpha-D-Gal Alpha-D-Glc Alpha-D-Gal-(1->3)-Alpha-D-Glc Escherichia coli
N
NO
Alpha-D-GalNAc Alpha-D-GalNAc Alpha-D-GalNAc-(1->3)-Alpha-D-GalNAc Escherichia coli
N
YES
Beta-D-Gal Alpha-D-GalNAc Beta-D-Gal-(1->3)-Alpha-D-GalNAc Escherichia coli
N
YES
Alpha-L-Fuc Beta-D-Gal Alpha-L-Fuc-(1->2)-Beta-D-Gal Escherichia coli
Y
YES
Alpha-D-Gal Beta-D-Gal Alpha-D-Gal-(1->3)-Beta-D-Gal Escherichia coli
N
YES
Beta-D-GalNAc Alpha-D-Gal Beta-D-GalNAc-(1->4)-Alpha-D-Gal Escherichia coli
N
YES

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