Team:Exeter/Results/biobricks

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Latest revision as of 02:17, 27 September 2012

BIOBRICKS SUBMITTED TO THE REGISTRY

Due to the time available we were only able to get 14 of our potential Biobricks into pSB1C3 and sent into the registry. Over 30 more were waiting for their chance. Our project was certainly worth more than the sum of it's Registry parts!

BBa_K764007 wbiP

Encodes the galactosytransferase wbiP that adds a β-D-Galactose donor sugar onto an α-D-GalNAc(N-Acetylgalactosamine) acceptor sugar to form a 1->3 glycosidic bond. wbiP readily glycosylates GalNAc analogues all with α substutions at the reducing end, and also glycosylates serine and threonine residues. It's close relatives include: WbnJ from Escherichia coli O86, wcmC from Escherichia coli O86, wbgO from Escherichia coli 055:H7, wfdH from Escherichia coli 0167, wbsK from Escherichia coli O128 and wfbZ from Escherichia coli O147.

This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession number: FM180568).

Sequence and Features

BBa_K764003 wfcA

Encodes the glucoronic acid transferase wfcA that adds a β-D-GlcA donor sugar onto an α-D-Mannose acceptor sugar to form a 1->2 glycosidic bond. It's close relatives include: wfeE from Escherichia coli O32, WfaO from Escherichia coli O24, wbhT from Escherichia coli O22 and wbaZ from Escherichia coli O9:K30.

This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession number: DQ868765).

Sequence and Features

BBa_K764002 wbnK

Encodes the fucosyltransferase wbnK that adds a branched α-L-Fucose donor sugar onto a β-D-Galactose acceptor sugar to form a 1->2 glycosidic bond. The protein wbnK has strict selectivity for Gal-β-(1->3)-GalNAc and acceptor specificity assays have shown that a change of glycosidic bond from 1->3 to 1->4 or from the β to the α configuration both lead to poor substrates for wbnK. wbnK is involved in the formation of both the O86 O-antigen and human blood group B antigen tetrasaccharide. It's close relatives include: wbwK from Escherichia coli O86:B7, wbgL from Escherichia coli O126, wbgN from Escherichia coli O55:H7 and wbgN from Escherichia coli O55:H6.

This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession number: AY670704).

Sequence and Features

BBa_K764000 wbnJ

Encodes the galactosytransferase wbnJ that adds a β-D-Galactose donor sugar onto an α-D-GalNAc(N-Acetylgalactosamine) acceptor sugar to form a 1->3 glycosidic bond. wbnJ is thought to be involved in colanic acid biosynthesis, acting as an acetyltransferase. It's close relatives include: wcmC from Escherichia coli O86:K2:H2, wfdH from Escherichia coli O167, wbsK from Escherichia coli O128, wbnA from Escherichia coli O113 and wbwJ from Escherichia coli O86:B7.

This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession number: AY667408).

Sequence and Features

BBa_K764004 wclY

Encodes the glycosyltransferase wclY from Escherichia coli O107 that adds an α-D-GlcNAc (N-Acetylglucosamine) donor sugar onto a β-D-Galactose acceptor sugar to form a 1->4 glycosidic bond. wclY has been identified as the glycosyltransferase that gives the differences between Escherichia coli O107 and O117 O-antigens. It's close relatives include: wclY from Escherichia coli O117 and wfeK from Escherichia coli O112ac.

This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession Number: EU694096).

Sequence and Features

BBa_K764033 TetR promoter_rbs_ompA_BBa_K322921-Term

A full construct of TetR promoter_rbs_SacB and (double) terminator (BBa_B0014) of Newcastle iGEM 2010's Bio-Brick BBa_K322921 using 3A assembly. The function of SacB remains unperturbed. This was linked to the signal peptide OmpA for export from the cell to prevent damage to Escherichia coli

.

Sequence and Features

BBa_K764034 pBAD/AraC strong promoter_rbs_ompA- BBa_K322921-Term

A full construct of pBAD/AraC weak promoter_rbs_SacB (BBa_K322921) and (double) terminator (BBa_B0014) using 3A assembly. The function of SacB remains unperturbed.

Sequence and Features

BBa_K764026 Cyclodextrin glycosyltransferase (cgt) + BBa_B0014

A construct of cgt (BBa_K764023) attached to a (double) terminator (BBa_B0014) using 3A assembly. The function of cyclodextrin glycosyltransferase remains unperturbed.

Sequence and Features

BBa_K76405 Hyaluronan synthase + BBa_B0014

A construct of HAS (BBa_K764022) attached to a (double) terminator (BBa_B0014) using 3A assembly. The function of hyaluronan synthase remains unperturbed.

Sequence and Features

BBa_K764024 BBa_K322921 + BBa_B0014

A construct of SacB attached to a (double) terminator (BBa_B0014) of Newcastle iGEM 2010's Bio-Brick BBa_K322921 using 3A assembly. The function of SacB remains unperturbed.

BBa_K764022 Hyaluronan synthase

Encodes hyaluronan synthase (hasA) that performs the following two reactions:

UDP-α-N-acetyl-D-glucosamine + β-D-glucuronosyl-(1->3)-N-acetyl-β-D-glucosaminyl-(1->4)-(nascent hyaluronan) = UDP + N-acetyl-β-D-glucosaminyl-(1->4)-β-D-glucuronosyl-(1->3)-N-acetyl-β-D-glucosaminyl-(1->4)-(nascent hyaluronan)

UDP-α-D-glucuronate + N-acetyl-β-D-glucosaminyl-(1->4)-β-D-glucuronosyl-(1->3)-(nascent hyaluronan) = UDP + β-D-glucuronosyl-(1->3)-N-acetyl-β-D-glucosaminyl-(1->4)-β-D-glucuronosyl-(1->3)-(nascent hyaluronan).

This generates hyaluronan, a virulence factor in streptococcus pyogenes if linked to lipid A molecules in the cell wall. Hyaluronan is also present in human joints and skin as a lubricant.

This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession Number: L20853).

Sequence and Features

BBa_K764023 Cyclodextrin glycosyltransferase (cgt)

Performs the enzymatic conversion of starch into variable sized cyclic oligosaccharides. This glycosyltransferase (cgt) from Bacillis sp 1011 produces alpha-cyclodextrin, a six membered ring of α-D-glucopyranoside units linked 1->4 glycosidic bonds.

This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession Number: 1942571).

Sequence and Features

BBa_K764009 wbnK + BBa_B0014

A construct of wbnK (BBa_K764002) attached to a (double) terminator (BBa_B0014) using 3A assembly. The function of wbnK remains unperturbed.

Sequence and Features

BBa_K764011 wclY + BBa_B0014

A construct of wclY (BBa_K764004) attached to a (double) terminator (BBa_B0014) using 3A assembly. The function of wclY remains unperturbed.

Sequence and Features

@@ Line 1: / Line 1: @@
 {{Template:Team:Exeter/e-candi_banner}}
-<p><b><u><a href="https://2012.igem.org/Team:Exeter/lab_book/1gp/wk1"; style="color:#57b947">GlycoBase/GlycoWeb</a></u></b>
-Due to the time available we were only able to get 14 of our potential Biobricks into pSB1C3 and sent into the registry. Over 30 more were waiting for there chance. Our project was certainly worth more than the sum of it's Registry parts!</font></p>
-<b><p>BBa_K764007 <i>WbiP</i></p></b>
-<p>Encodes the galactosytransferase <i>wbiP</i> that adds a β-D-Galactose donor sugar onto an α-D-GalNAc(N-Acetylgalactosamine) acceptor sugar to form a 1->3 glycosidic bond. </p>
+<p><b><big><div style="text-align: center;"><span style="color:#57B947">BIOBRICKS SUBMITTED TO THE REGISTRY</span></div></big></b></p>
+<p>Due to the time available we were only able to get 14 of our potential Biobricks into pSB1C3 and sent into the registry. Over 30 more were waiting for their chance. Our project was certainly worth more than the sum of it's Registry parts!</p>
+<b><p>BBa_K764007 <i>wbiP</i></p></b>
+<p>Encodes the galactosytransferase <i>wbiP</i> that adds a β-D-Galactose donor sugar onto an α-D-GalNAc(N-Acetylgalactosamine) acceptor sugar to form a 1->3 glycosidic bond. <i>wbiP</i> readily glycosylates GalNAc analogues all with α substutions at the reducing end, and also glycosylates serine and threonine residues. It's close relatives include: <i>WbnJ</i> from <i>Escherichia coli</i> O86, <i>wcmC</i> from <i>Escherichia coli</i> O86, <i>wbgO</i> from <i>Escherichia coli</i> 055:H7, <i>wfdH</i> from <i>Escherichia coli</i> 0167, <i>wbsK</i> from <i>Escherichia coli</i> O128  and <i>wfbZ</i> from <i>Escherichia coli</i> O147.</p>
+<p> This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession number: FM180568).</p>
+<span class='h3bb'>'''Sequence and Features'''</span>
+<partinfo>BBa_K764007</partinfo>
 <b><p>BBa_K764003 <i>wfcA</i></p></b>
-<p>Encodes the glucoronic acid transferase <i>wfcA</i> that adds a β-D-GlcA donor sugar onto an α-D-Mannose acceptor sugar to form a 1->2 glycosidic bond. </p>
+<p>Encodes the glucoronic acid transferase <i>wfcA</i> that adds a β-D-GlcA donor sugar onto an α-D-Mannose acceptor sugar to form a 1->2 glycosidic bond. It's close relatives include: <i>wfeE</i> from <i>Escherichia coli</i> O32, <i>WfaO</i> from <i>Escherichia coli</i> O24, <i>wbhT</i> from <i>Escherichia coli</i> O22 and <i>wbaZ</i> from <i>Escherichia coli</i> O9:K30.</p>
+<p> This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession number: DQ868765).</p>
+<span class='h3bb'>'''Sequence and Features'''</span>
+<partinfo>BBa_K764003</partinfo>
 <b><p>BBa_K764002 <i>wbnK</i></p></b>
-<p>Encodes the fucosyltransferase <i>wbnK</i> that adds a branched α-L-Fucose donor sugar onto a β-D-Galactose acceptor sugar to form a 1->2 glycosidic bond. </p>
+<p>Encodes the fucosyltransferase <i>wbnK</i> that adds a branched α-L-Fucose donor sugar onto a β-D-Galactose acceptor sugar to form a 1->2 glycosidic bond. The protein wbnK has strict selectivity for Gal-β-(1->3)-GalNAc and acceptor specificity assays have shown that a change of glycosidic bond from 1->3 to 1->4 or from the β to the α configuration both lead to poor substrates for wbnK. wbnK is involved in the formation of both the O86 O-antigen and human blood group B antigen tetrasaccharide. It's close relatives include: <i>wbwK</i> from <i>Escherichia coli</i> O86:B7, <i>wbgL</i> from <i>Escherichia coli</i> O126, <i>wbgN</i> from <i>Escherichia coli</i> O55:H7 and <i>wbgN</i> from <i>Escherichia coli</i> O55:H6.</p>
+<p> This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession number: AY670704).</p>
+<span class='h3bb'>'''Sequence and Features'''</span>
+<partinfo>BBa_K764002</partinfo>
 <b><p>BBa_K764000 <i>wbnJ</i></p></b>
-<p>Encodes the galactosytransferase <i>wbnJ</i> that adds a β-D-Galactose donor sugar onto an α-D-GalNAc(N-Acetylgalactosamine) acceptor sugar to form a 1->3 glycosidic bond. </p>
+<p>Encodes the galactosytransferase <i>wbnJ</i> that adds a β-D-Galactose donor sugar onto an α-D-GalNAc(N-Acetylgalactosamine) acceptor sugar to form a 1->3 glycosidic bond. <i>wbnJ</i> is thought to be involved in colanic acid biosynthesis, acting as an acetyltransferase. It's close relatives include: <i>wcmC</i> from <i>Escherichia coli</i> O86:K2:H2, <i>wfdH</i> from <i>Escherichia coli</i> O167, <i>wbsK</i> from <i>Escherichia coli</i> O128, <i>wbnA</i> from <i>Escherichia coli</i> O113 and <i>wbwJ</i> from <i>Escherichia coli</i> O86:B7.</p>
-<b><p>BBa_K764004 WclY</i></p></b>
+<p> This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession number: AY667408).</p>
-<p>Encodes the glycosyltransferase <i>wclY</i> that adds an α-D-GlcNAc (N-Acetylglucosamine) donor sugar onto a β-D-Galactose acceptor sugar to form a 1->4 glycosidic bond. </p>
+<span class='h3bb'>'''Sequence and Features'''</span>
-<b><p>BBa_K764033 Tetr promoter_rbs_ompA_BBa_K322921-Term</p></b>
+<partinfo>BBa_K764000</partinfo>
-<b><p>BBa_K764034 Pbad Weak promoter_rbs_ompA- BBa_K322921-Term</p></b>
+<b><p>BBa_K764004 <i>wclY</i></p></b>
+<p>Encodes the glycosyltransferase <i>wclY</i> from <i>Escherichia coli</i> O107 that adds an α-D-GlcNAc (N-Acetylglucosamine) donor sugar onto a β-D-Galactose acceptor sugar to form a 1->4 glycosidic bond. <i>wclY</i> has been identified as the glycosyltransferase that gives the differences between <i>Escherichia coli</i> O107 and O117 O-antigens. It's close relatives include: <i>wclY</i> from <i>Escherichia coli</i> O117 and <i>wfeK</i> from <i>Escherichia coli</i> O112ac.</p>
-<b><p>BBa_K764026 Cyclodextrin glycosyltransferase + BBa_B0014</p></b>
+<p> This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession Number: EU694096).</p>
+<span class='h3bb'>'''Sequence and Features'''</span>
-<b><p>BBa_K764025 Hyaluronan synthase + BBa_B0014 </p></b>
+<partinfo>BBa_K764004</partinfo>
+<b><p>BBa_K764033 TetR promoter_rbs_ompA_BBa_K322921-Term</p></b>
+<p> A full construct of TetR promoter_rbs_<i>SacB</i> and (double) terminator (BBa_B0014) of Newcastle iGEM 2010's Bio-Brick BBa_K322921 using 3A assembly. The function of SacB remains unperturbed. This was linked to the signal peptide OmpA for export from the cell to prevent damage to <i>Escherichia coli</i></p>.
+<span class='h3bb'>'''Sequence and Features'''</span>
+<partinfo>BBa_K764033</partinfo>
+<b><p>BBa_K764034 pBAD/AraC strong promoter_rbs_ompA- BBa_K322921-Term</p></b>
+<p> A full construct of pBAD/AraC weak promoter_rbs_<i>SacB</i> (BBa_K322921) and (double) terminator (BBa_B0014) using 3A assembly. The function of SacB remains unperturbed.</p>
+<span class='h3bb'>'''Sequence and Features'''</span>
+<partinfo>BBa_K764034</partinfo>
+<b><p>BBa_K764026 Cyclodextrin glycosyltransferase (cgt) + BBa_B0014</p></b>
+<p> A construct of <i>cgt</i> (BBa_K764023) attached to a (double) terminator (BBa_B0014) using 3A assembly. The function of cyclodextrin glycosyltransferase remains unperturbed.</p>
+<span class='h3bb'>'''Sequence and Features'''</span>
+<partinfo>BBa_K764026</partinfo>
+<b><p>BBa_K76405 Hyaluronan synthase + BBa_B0014 </p></b>
+<p> A construct of <i>HAS</i> (BBa_K764022) attached to a (double) terminator (BBa_B0014) using 3A assembly. The function of hyaluronan synthase remains unperturbed.</p>
+<span class='h3bb'>'''Sequence and Features'''</span>
+<partinfo>BBa_K764025</partinfo>
 <b><p>BBa_K764024 BBa_K322921 + BBa_B0014 </p></b>
+<p> A construct of <i>SacB</i> attached to a (double) terminator (BBa_B0014) of Newcastle iGEM 2010's Bio-Brick BBa_K322921 using 3A assembly. The function of SacB remains unperturbed.</p>
+<partinfo>BBa_K764024</partinfo>
@@ Line 47: / Line 123: @@
 <p>Encodes hyaluronan synthase (hasA) that performs the following two reactions: </p>
 <p>UDP-α-N-acetyl-D-glucosamine + β-D-glucuronosyl-(1->3)-N-acetyl-β-D-glucosaminyl-(1->4)-(nascent hyaluronan) = UDP + N-acetyl-β-D-glucosaminyl-(1->4)-β-D-glucuronosyl-(1->3)-N-acetyl-β-D-glucosaminyl-(1->4)-(nascent hyaluronan) </p>
-<p>UDP-α-D-glucuronate + N-acetyl-β-D-glucosaminyl-(1->4)-β-D-glucuronosyl-(1->3)-(nascent hyaluronan) = UDP + β-D-glucuronosyl-(1->3)-N-acetyl-β-D-glucosaminyl-(1->4)-β-D-glucuronosyl-(1->3)-(nascent hyaluronan). </p>
+<p>UDP-α-D-glucuronate + N-acetyl-β-D-glucosaminyl-(1->4)-β-D-glucuronosyl-(1->3)-(nascent hyaluronan) = UDP + β-D-glucuronosyl-(1->3)-N-acetyl-β-D-glucosaminyl-(1->4)-β-D-glucuronosyl-(1->3)-(nascent hyaluronan).</p>
+<p>This generates hyaluronan, a virulence factor in streptococcus pyogenes if linked to lipid A molecules in the cell wall. Hyaluronan is also present in human joints and skin as a lubricant.</p>
+<p> This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession Number: L20853).</p>
-<b><p>BBa_K764023 Cyclodextrin glycosyltransferase </p></b>
+<span class='h3bb'>'''Sequence and Features'''</span>
-<p>Encodes the cyclodextrin glycosyltransferase cgt that cyclises part of a (1->4)-α-D-glucan chain by formation of a (1->4)-α-D-glucosidic bond. </p>
+<partinfo>BBa_K764022</partinfo>
-<b><p>BBa_K764009 <i>wclY</i> + BBa_B0014 </p></b>
+<b><p>BBa_K764023 Cyclodextrin glycosyltransferase (cgt) </p></b>
+<p>Performs the enzymatic conversion of starch into variable sized cyclic oligosaccharides. This glycosyltransferase (cgt) from Bacillis sp 1011 produces alpha-cyclodextrin, a six membered ring of α-D-glucopyranoside units linked 1->4 glycosidic bonds.</p>
+<p> This gene was synthesised by reverse translating the amino acid sequence by codon-optimisation (Accession Number: 1942571).</p>
+<span class='h3bb'>'''Sequence and Features'''</span>
+<partinfo>BBa_K764023</partinfo>
+<b><p>BBa_K764009 <i>wbnK</i> + BBa_B0014 </p></b>
+<p> A construct of <i>wbnK</i> (BBa_K764002) attached to a (double) terminator (BBa_B0014) using 3A assembly. The function of wbnK remains unperturbed.</p>
+<span class='h3bb'>'''Sequence and Features'''</span>
+<partinfo>BBa_K764009</partinfo>
 <b><p>BBa_K764011 <i>wclY</i> + BBa_B0014</p></b>
+<p> A construct of <i>wclY</i> (BBa_K764004) attached to a (double) terminator (BBa_B0014) using 3A assembly. The function of wclY remains unperturbed.</p>
+<span class='h3bb'>'''Sequence and Features'''</span>
+<partinfo>BBa_K764011</partinfo>