Team:Grinnell/Attributions

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<h1>DspB</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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<h1>Attributions</h1>
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<h2>References</h2>
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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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<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>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="Davis"></a><b>Davies, D. G., Parsek, M. R., Pearson, J. P., Iglewski, B. H., Costerton, J. W., & Greenberg, E. P.</b> 1998. The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science. <b>280</b>(11):295-298.</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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<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="Foley & Gilbert"></a><b>Foley & Gilbert </b> 1996. Antibiotic resistance of biofilms. Biofouling. <b>10</b>(16):331-346.</li>
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<li><a name="Gilchrist et al."></a><b>Gilchrist, A., JA Fisher, and J. Smit </b> 1992. Nucleotide
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sequence analysis of the gene encoding the Caulobacter crescentus paracrystalline surface
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layer protein.CJ Microbiol. <b>38</b>(16):193-202.</li>
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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="Laub"></a><b>Laub, M., L. Shapiro, and H. McAdams.</b> 2007. Systems Biology of <i>Caulobacter</i> Annu. Rev. Genet. <b>41</b>:429-441.</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="Mittelman"></a><b>Mittelman, M. W.</b> 1998. Structure and functional characteristics of bacterial biofilms in fluid processing operations. J. of Dairy Science. <b>81</b>:2760-2764.</li>
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                        <li><a name="Moon et al."></a><b>Moon et al.</b> 2001. Isolation and Characterization of a Highly Specific Serine Endopeptidase from an Oral Strain of <i>Staphylococcus epidermidis</i>. Biological Chemistry. <b>382</b>(7):1095-1099.</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="Nomellinii"></a><b>Nomellini, J., M. Toporowski and J. Smit.</b> 2004. Secretion or Presentation of Recombinant Proteins and Peptides Mediated by the S-layer of <i>Caulobacter crescentus</i>. in <b>Protein Expression Technologies: Current Status and Future Trends</b> F. Baneyx Edit. 477-524.</li>
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<li><a name="Ryn"></a><b>Ryan, K.R., Taylor, J.A, and Bowers, L.M.</b> 2009. The Bam complex subunit BamE (SmpA) is required for membrane integrity, stalk growth and normal levels of outer membrane β-barrel proteins in <i>Caulobacter crescentus</i> Microbiology. <b>156</b>:742-756.</li>
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<li><a name="Simoes1"></a><b>Sim&otilde;es and M.J. Vieira.</b> 2009. Persister cells in Pseudomonas fluorescens biofilms treated with a biocide. In Proceedings of the international conference processes in biofilms: Fundamentals to applications 58–62, Davis, CA.</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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<li><a name="Toh"></a><b>Toh et al.</b> 2008. Characterization of the Caulobacter crescentus Holdfast Polysaccharide Biosynthesis Pathway Reveals Significant Redundancy in the
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Initiating Glycosyltransferase and Polymerase Steps. J. of Bacteriology <b>190</b>(21):7219–7231.</li>
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<h2>Attributions and Contributions</h2>
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<p>We would like to thank the <a href="https://2010.igem.org/Team:British_Columbia">University of British Columbia</a> 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 <a href="http://www.grinnell.edu/academic/biology">Grinnell College Biology Department</a> for providing us with access to instruments and materials for our project. We thank <a href="http://www.idtdna.com/Home/Home.aspx">Integrated DNA Technologies (IDT)</a> for generously supporting us with oligos and for synthesizing our two genes, <i>esp</i> and <i>dspB</i>, with codons optimized for expression in <i>Caulobacter</i>.
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Latest revision as of 04:38, 29 September 2011

Grinnell Menubar

References

Attributions

References

  • Awram, P., and J. Smit. 1998. The Caulobacter crescentus paracrystalline S-layer protein is secreted by an ABC transporter (type I) secretion apparatus. J. of Bacteriol. 180(12):3062-69.
  • Bingle, W.H., J.F. Nomellini, and J. Smit. 2000. Secretion of the Caulobacter crescentus S-layer protein: further localization of the C-terminal secretion signal and its use for secretion of recombinant proteins. J. of Bacteriol. 182(11):3298-301.
  • Davies, D. G., Parsek, M. R., Pearson, J. P., Iglewski, B. H., Costerton, J. W., & Greenberg, E. P. 1998. The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science. 280(11):295-298.
  • Foley & Gilbert 1996. Antibiotic resistance of biofilms. Biofouling. 10(16):331-346.
  • Gilchrist, A., JA Fisher, and J. Smit 1992. Nucleotide sequence analysis of the gene encoding the Caulobacter crescentus paracrystalline surface layer protein.CJ Microbiol. 38(16):193-202.
  • Kaplan, J., C. Ragunath, N. Ramasubbu, and D. Fine. 2003. Detachment of Actinobacillus actinomycetemcomitans Biofilm Cells by an Endogenous beta-Hexosaminidase Activity. J. of Bacteriol. 185(16):4693-4698.
  • Laub, M., L. Shapiro, and H. McAdams. 2007. Systems Biology of Caulobacter Annu. Rev. Genet. 41:429-441.
  • Lu, T., and J. Collins. 2007. Dispersing biofilms with engineered enzymatic bacteriophage. PNAS 104(27):11197-11202.
  • Malakooti, J., S. Wang, and B. Ely. 1995. A Consensus Promoter Sequence for Caulobacter crescentus Genes Involved in Biosynthetic and Housekeeping Functions. J. of Bacteriol. 177(15):4372-4376.
  • Manuel, S.G.A., C. Ragunath, H. Sait, E. Izano, J. Kaplan, and N. Ramasubbu. 2007. Role of active-site residues of dispersin B, a biofilm-releasing β-hexosaminidase from a periodontal pathogen, in substrate hydrolysis. FEBS J. 274:5987-5999.
  • Meisenzahl, A., L. Shapiro, U. Jenal. 1997. Isolation and Characterization of a Xylose-Dependent Promoter from Caulobacter crescentus. J. of Bacteriol. 179(3):592-600.
  • Mittelman, M. W. 1998. Structure and functional characteristics of bacterial biofilms in fluid processing operations. J. of Dairy Science. 81:2760-2764.
  • Moon et al. 2001. Isolation and Characterization of a Highly Specific Serine Endopeptidase from an Oral Strain of Staphylococcus epidermidis. Biological Chemistry. 382(7):1095-1099.
  • Nomellini, J., C. Li, D. Lavallee, I. Shanina, L. Cavacini, M. Horwitz, and J. Smit. 2010. Development of an HIV-1 Specific Microbicide Using Caulobacter crescentus S-Layer Mediated Display of CD4 and MIP1α. PLoS ONE 5(4):e10366.
  • Nomellini, J., M. Toporowski and J. Smit. 2004. Secretion or Presentation of Recombinant Proteins and Peptides Mediated by the S-layer of Caulobacter crescentus. in Protein Expression Technologies: Current Status and Future Trends F. Baneyx Edit. 477-524.
  • Ryan, K.R., Taylor, J.A, and Bowers, L.M. 2009. The Bam complex subunit BamE (SmpA) is required for membrane integrity, stalk growth and normal levels of outer membrane β-barrel proteins in Caulobacter crescentus Microbiology. 156:742-756.
  • Simões and M.J. Vieira. 2009. Persister cells in Pseudomonas fluorescens biofilms treated with a biocide. In Proceedings of the international conference processes in biofilms: Fundamentals to applications 58–62, Davis, CA.
  • Simões, M., L. Simões, and M.J. Vieira. 2010. A review of current and emergent biofilm control strategies. Food Sci. and Tech. 43:573-583.
  • Toh et al. 2008. Characterization of the Caulobacter crescentus Holdfast Polysaccharide Biosynthesis Pathway Reveals Significant Redundancy in the Initiating Glycosyltransferase and Polymerase Steps. J. of Bacteriology 190(21):7219–7231.

Attributions and Contributions

We would like to thank the University of British Columbia for providing a copy of the wild type dspB 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 Integrated DNA Technologies (IDT) for generously supporting us with oligos and for synthesizing our two genes, esp and dspB, with codons optimized for expression in Caulobacter.

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