Team:Grinnell/Attributions

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<title>DspB</title>
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<h1>DspB</h1>
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<h1>Attributions</h1>
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<p>DspB has been isolated and purified and has been shown to increase dissemination of wild type cells from biofilms and restore dissemination in mutant cells (<a href="https://2011.igem.org/Team:Grinnell/Attributions#Kaplan">Kaplan 2003</a>).</p>
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<h2>References</h2>
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<p>DspB comes from the bacteria <i>Aggregatibacter actinomycetemcomitans</i>.  It is most likely an N-acetylglucosaminidase that causes the detachment of cells from biofilm colonies through the 1→ 4 glycosidic bond of β-substituted N-acetylglucosamine (<a href="https://2011.igem.org/Team:Grinnell/Attributions#Kaplan">Kaplan 2003</a>). DspB is homologous to family 20 glycosyl hydrolases which cleave terminal monosaccharide residues (<a href="https://2011.igem.org/Team:Grinnell/Attributions#Kaplan">Kaplan 2003</a>).</p>
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<li><a name="Awram"></a><b>Awram, P., and J. Smit.</b> 1998. The <i>Caulobacter crescentus</i> paracrystalline S-layer protein is secreted by an ABC transporter (type I) secretion apparatus. J. of Bacteriol. <b>180</b>(12):3062-69.<!--10-12% of total protein synthesis--></li>
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<p>One possible substrate for DspB is a type IV pilus required for the attachment and autoaggregation of bacteria by altering its adhesive properties. Another possible substrate is exopolymeric substance (EPS) which is part of the exopolysaccharide matrix which plays a role in biofilm formation.  Exopolysaccharides may contain N-acetylglucosamine which DspB is thought to hydrolyze. <a href="https://2011.igem.org/Team:Grinnell/Attributions#Manuel">Manuel et. al</a> have characterized the mechanistic aspects of DspB and show that conserved D183 and E184 resemble the proposed 20 β-hexosaminidase mechanism; that aromatic residues W237, Y278 and D183 assist N-acetal group orientation and hydrolysis; that Y187 plays a role in specificity; and that residues R27, E332 and W330 help stabilize the transition state of hydrolysis (<a href="https://2011.igem.org/Team:Grinnell/Attributions#Manuel">Manuel 2007</a>).</p>
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<li><a name="Bingle"></a><b>Bingle, W.H., J.F. Nomellini, and J. Smit.</b> 2000. Secretion of the <i>Caulobacter crescentus</i> S-layer protein: further localization of the C-terminal secretion signal and its use for secretion of recombinant proteins. J. of Bacteriol. <b>182</b>(11):3298-301.</li>
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<p>We will test two versions of the gene.  The WT gene was sent to us by the <a href="https://2010.igem.org/Team:British_Columbia">University of British Columbia 2010 iGEM Team</a> and was already cloned into pSB1C3.  The second is a synthetic version codon optimized for expression in <i>Caulobacter</i>.  This gene was synthesized by <a href="http://www.idtdna.com/Home/Home.aspx">IDT</a>. Optimized <i>dspB</i> is <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K531004">Part:BBa_K531004</a>.</p>
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<li><a name="Kaplan"></a><b>Kaplan, J., C. Ragunath, N. Ramasubbu, and D. Fine.</b> 2003. Detachment of <i>Actinobacillus actinomycetemcomitans</i> Biofilm Cells by an Endogenous beta-Hexosaminidase Activity. J. of Bacteriol. <b>185</b>(16):4693-4698.</li>
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<li><a name="Lu"></a><b>Lu, T., and J. Collins.</b> 2007. Dispersing biofilms with engineered enzymatic bacteriophage. PNAS <b>104</b>(27):11197-11202.</li>
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<li><a name="Malakooti"></a><b>Malakooti, J., S. Wang, and B. Ely.</b> 1995. A Consensus Promoter Sequence for <i>Caulobacter crescentus</i> Genes Involved in Biosynthetic and Housekeeping Functions. J. of Bacteriol. <b>177</b>(15):4372-4376.</li>
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<li><a name="Manuel"></a><b>Manuel, S.G.A., C. Ragunath, H. Sait, E. Izano, J. Kaplan, and N. Ramasubbu.</b> 2007. Role of active-site residues of dispersin B, a biofilm-releasing β-hexosaminidase from a periodontal pathogen, in substrate hydrolysis. FEBS J. <b>274</b>:5987-5999.</li>
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<li><a name="Mesenzahl"></a><b>Meisenzahl, A., L. Shapiro, U. Jenal.</b> 1997. Isolation and Characterization of a Xylose-Dependent Promoter from <i>Caulobacter crescentus</i>. J. of Bacteriol. <b>179</b>(3):592-600.</li>
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<li><a name="Nomellini"></a><b>Nomellini, J., C. Li, D. Lavallee, I. Shanina, L. Cavacini, M. Horwitz, and J. Smit.</b> 2010. Development of an HIV-1 Specific Microbicide Using <i>Caulobacter crescentus</i> S-Layer Mediated Display of CD4 and MIP1&alpha;. PLoS ONE <b>5</b>(4):e10366.</li>
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<li><a name="Simoes"></a><b>Sim&otilde;es, M., L. Sim&otilde;es, and M.J. Vieira.</b> 2010. A review of current and emergent biofilm control strategies. Food Sci. and Tech. <b>43</b>:573-583.</li>
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<h2>Attributions and Contributions</h2>
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<p>We would like to thank the University of British Columbia for providing a copy of the wild type <i>dspB</i> gene.  We would also like to thank Dr. Lisa Bowers for her enduring support, guidance, and teaching us our way around the lab.  Also thank you to Carolyn Bosse, Kathy Miller, and the Grinnell College Biology Department for providing us with access to instruments and materials for our project.  We thank <a href="http://www.idtdna.com/Home/Home.aspx">IDT</a> for their generous <a href="https://2011.igem.org/Team:Grinnell/Attributions/Sponsors">sponsorship</a> of our team.</p>
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Revision as of 20:37, 28 September 2011

Grinnell Menubar

DspB

DspB

DspB has been isolated and purified and has been shown to increase dissemination of wild type cells from biofilms and restore dissemination in mutant cells (Kaplan 2003).

DspB comes from the bacteria Aggregatibacter actinomycetemcomitans. It is most likely an N-acetylglucosaminidase that causes the detachment of cells from biofilm colonies through the 1→ 4 glycosidic bond of β-substituted N-acetylglucosamine (Kaplan 2003). DspB is homologous to family 20 glycosyl hydrolases which cleave terminal monosaccharide residues (Kaplan 2003).

One possible substrate for DspB is a type IV pilus required for the attachment and autoaggregation of bacteria by altering its adhesive properties. Another possible substrate is exopolymeric substance (EPS) which is part of the exopolysaccharide matrix which plays a role in biofilm formation. Exopolysaccharides may contain N-acetylglucosamine which DspB is thought to hydrolyze. Manuel et. al have characterized the mechanistic aspects of DspB and show that conserved D183 and E184 resemble the proposed 20 β-hexosaminidase mechanism; that aromatic residues W237, Y278 and D183 assist N-acetal group orientation and hydrolysis; that Y187 plays a role in specificity; and that residues R27, E332 and W330 help stabilize the transition state of hydrolysis (Manuel 2007).

We will test two versions of the gene. The WT gene was sent to us by the University of British Columbia 2010 iGEM Team and was already cloned into pSB1C3. The second is a synthetic version codon optimized for expression in Caulobacter. This gene was synthesized by IDT. Optimized dspB is Part:BBa_K531004.

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