Difference between revisions of "Team:Toulouse-INSA-UPS/Description"
| Line 51: | Line 51: | ||
<!--PART 1 --> | <!--PART 1 --> | ||
<div class="tab-pane fade show active" id="Desc_Part1" role="tabpanel"> | <div class="tab-pane fade show active" id="Desc_Part1" role="tabpanel"> | ||
| − | <h2 class="heavy">Cellulose: a | + | <h2 class="heavy">Cellulose: a Material with Endless Possibilities</h2><hr/> |
<figure class="figure" style="text-align:center;"> | <figure class="figure" style="text-align:center;"> | ||
<img style="width : 70%; heigth = auto;" src="https://static.igem.org/mediawiki/2018/2/26/T--Toulouse-INSA-UPS--Desc--Youn--Cellulosemolecule.png" class="figure-img img-fluid rounded" alt="A generic square placeholder image with rounded corners in a figure."> | <img style="width : 70%; heigth = auto;" src="https://static.igem.org/mediawiki/2018/2/26/T--Toulouse-INSA-UPS--Desc--Youn--Cellulosemolecule.png" class="figure-img img-fluid rounded" alt="A generic square placeholder image with rounded corners in a figure."> | ||
<figcaption class="figure-caption"><strong>Figure 1:</strong> Cellulose melecular model </figcaption> | <figcaption class="figure-caption"><strong>Figure 1:</strong> Cellulose melecular model </figcaption> | ||
</figure> | </figure> | ||
| − | <p>With approximatively fifty billion tonnes produced yearly, cellulose is | + | <p>With approximatively fifty billion tonnes produced yearly, cellulose is the most abundant bio-polymers on earth. Cellulose is a linear polysaccharide of D-glucose residues linked to each other via β-1,4 bonds. It is mainly synthetized in the plant cell wall, associated with other molecules, in order to shape plant body. However, cellulose is also secreted in the surrounding of aerobic bacteria such as <em>Gluconacetobacter hansenii </em>in order to form a bio-film enabling oxygen uptake. Nowadays, cellulose and its derivatives (nitrocellulose, cellulose acetate, methyl cellulose, carboxymethyl cellulose, etc…) are among the first materials that have been intensively used in industries (wood, cotton, textiles, paper, electronics and biomedical devices<sup>1</sup>), representing a market size evaluated at USD 20.61 billion in 2015.</p> |
| − | + | <p>Bacterial cellulose has also been the target of the research and development in industries. As it is naturally purer than plant cellulose, it doesn’t need to go through harsh purification processes that cost a lot of energy, time and money<sup>2>/sup>. However, different types of cellulose with various properties and degrees of purity are used in the industry, which explains the advantage of having a system that could manage with different type of cellulose.</p> | |
| − | + | <p>By functionalising cellulose, we aim to demonstrate how this widely used material can be more than a simple packaging or textile fibres. By combining it to our protein platform Cerberus, cellulose can become a source of information and bring new opportunities for industrial applications. </p> | |
| − | + | ||
| + | |||
| + | <h3>References</h3> | ||
| + | <ol> | ||
| + | <li>Keshk SM: Bacterial Cellulose Production and its Industrial Applications. Journal of Bioprocessing & Biotechniques 2014, 4;2. DOI: 10.4172/2155-9821.1000150.</li> | ||
| + | <li>Faezah Esa SMT, Norliza Abd Rahman: Overview of Bacterial Cellulose Production and Application. Agriculture and Agricultural Science Procedia 2 2104:113-119. DOI: 10.1016/j.aaspro.2014.11.017.</li> | ||
| + | </ol> | ||
| + | <i> | ||
| + | <ol style=" font-size:15px;"> | ||
| + | <li> Serge Perez, (2000), Structure et morphologie de la cellulose.</li> | ||
| + | <li> Keshk SMAS (2014) Bacterial Cellulose Production and its Industrial Applications. J Bioprocess Biotech 4: 150 doi: 10.4172/2155-9821.1000150 | ||
| + | <li> « Overview of Bacterial Cellulose Production and Application », Agric. Agric. Sci. Procedia, vol. 2, p. 113-119, janv. 2014. | ||
| + | </ol> | ||
| + | </i> | ||
</div> | </div> | ||
| Line 74: | Line 87: | ||
<p>When brainstorming about the project, we had these different ideas and they all revolved around functionalising several materials. We then realised it could be of great use to have one material that we could functionalise at our discretion. That is how we decided to work on cellulose, especially bacterial cellulose, in hope of developing its use by adding a whole range of exciting possibilities. From conductive paper to anti-infection tissues, applications domains are aplenty (medicine, textile, stationery, etc). The major bottleneck is the complexity to conjugate bioactive molecules to cellulose.</p> | <p>When brainstorming about the project, we had these different ideas and they all revolved around functionalising several materials. We then realised it could be of great use to have one material that we could functionalise at our discretion. That is how we decided to work on cellulose, especially bacterial cellulose, in hope of developing its use by adding a whole range of exciting possibilities. From conductive paper to anti-infection tissues, applications domains are aplenty (medicine, textile, stationery, etc). The major bottleneck is the complexity to conjugate bioactive molecules to cellulose.</p> | ||
<p>To circumvent this limitation and enable a wide range of chemicals to be fixated to cellulose, we designed a three headed linker protein named Cerberus (in reference to the mythological dog). Cerberus is based on the fusion of three fixating protein structures representing the three heads of the system. The first head is a protein domain of the type 3 Carbohydrate Binding Module (CBM3) family to bind cellulose. The second is one of the strongest linkage systems of the living realm, streptavidin, with its high affinity for biotinylated compounds. The last of the heads features a non-natural amino acid, 4-L-azidophenylalanine, catalysing covalent bonds by click chemistry. Therefore, the versatility of our thought-out linker will allow a large variety of organic and inorganic molecules to conjugate with cellulose.</p> | <p>To circumvent this limitation and enable a wide range of chemicals to be fixated to cellulose, we designed a three headed linker protein named Cerberus (in reference to the mythological dog). Cerberus is based on the fusion of three fixating protein structures representing the three heads of the system. The first head is a protein domain of the type 3 Carbohydrate Binding Module (CBM3) family to bind cellulose. The second is one of the strongest linkage systems of the living realm, streptavidin, with its high affinity for biotinylated compounds. The last of the heads features a non-natural amino acid, 4-L-azidophenylalanine, catalysing covalent bonds by click chemistry. Therefore, the versatility of our thought-out linker will allow a large variety of organic and inorganic molecules to conjugate with cellulose.</p> | ||
| − | + | ||
</div> | </div> | ||
| Line 84: | Line 97: | ||
<figcaption class="figure-caption"><strong>Figure 1:</strong> Representation of CtCBM3a associated with cellulose microfibrills. CtCBM3a is colored in cyan and orange. Amino acids involved in stacking with glucose units of cellulose is in magenta (from pdb 1NBC). Cellulose is in green (from Perez and Samain, 2010 doi.org/10.1016/S0065-2318(10)64003-6).</figcaption> | <figcaption class="figure-caption"><strong>Figure 1:</strong> Representation of CtCBM3a associated with cellulose microfibrills. CtCBM3a is colored in cyan and orange. Amino acids involved in stacking with glucose units of cellulose is in magenta (from pdb 1NBC). Cellulose is in green (from Perez and Samain, 2010 doi.org/10.1016/S0065-2318(10)64003-6).</figcaption> | ||
</figure> | </figure> | ||
| − | <p>The first head is the core of our linker, Cerberus. We chose the Carbohydrate Binding Module type 3a (CBM3a) to bind to cellulose. This domain is found in the cellulosome of <i>Clostridium thermocellum</i><SUP> | + | <p>The first head is the core of our linker, Cerberus. We chose the Carbohydrate Binding Module type 3a (CBM3a) to bind to cellulose. This domain is found in the cellulosome of <i>Clostridium thermocellum</i><SUP>1</SUP> and its four aromatic amino acids make it the perfect candidate to bind to cellulose through a dipole-dipole interaction between the CBM3a’s aromatic amino acids and the cellulose’s glucose rings.</p> |
<p>Our CBM3a features a long endogenous linker on each end, to which we can attach other structures to functionalise cellulose.</p> | <p>Our CBM3a features a long endogenous linker on each end, to which we can attach other structures to functionalise cellulose.</p> | ||
| − | + | <h3>References</h3> | |
| + | |||
| + | <i> | ||
| + | <ol style=" font-size:15px;"> | ||
| + | <li> E. Morag et al., « Expression, purification, and characterization of the cellulose-binding domain of the scaffoldin subunit from the cellulosome of Clostridium thermocellum. », Appl. Environ. Microbiol., vol. 61, no 5, p. 1980-1986, mai 1995. | ||
| + | </ol> | ||
| + | </i> | ||
</div> | </div> | ||
| Line 99: | Line 118: | ||
<p>The second head of Cerberus is streptavidin, which has been added to cellulose N-Terminus. Streptavidin is a 60 kDa homotetrameric protein, isolated from <i>Streptomyces avidinii</i>, and it is well known for its interaction with biotin and biotinylated proteins. With a dissociation constant of 10<sup>-13</sup> M, the interaction between streptavidin and biotin is the strongest non-covalent one known in Nature<SUP>5</SUP>.</p> | <p>The second head of Cerberus is streptavidin, which has been added to cellulose N-Terminus. Streptavidin is a 60 kDa homotetrameric protein, isolated from <i>Streptomyces avidinii</i>, and it is well known for its interaction with biotin and biotinylated proteins. With a dissociation constant of 10<sup>-13</sup> M, the interaction between streptavidin and biotin is the strongest non-covalent one known in Nature<SUP>5</SUP>.</p> | ||
<p>The sequence of streptavidin wild type is used in fusion with the CBM3a. This streptavidin forms a complex with three other streptavidin monomers, hence the unmatched affinity for biotin since it can bind four molecules of biotin per tetramer. We decided to use two versions of streptavidin: the native form which is tetrameric because we have data on its interaction with biotin, and a monomeric version called mSA2<SUP>6</SUP> because we feared that the tetrameric streptavidin would cause agglutination of our Cerberus protein. In case we needed to release the streptavidin linked to our function into the surrounding medium, we also included a TEV-protease site to cut off this section.</p> | <p>The sequence of streptavidin wild type is used in fusion with the CBM3a. This streptavidin forms a complex with three other streptavidin monomers, hence the unmatched affinity for biotin since it can bind four molecules of biotin per tetramer. We decided to use two versions of streptavidin: the native form which is tetrameric because we have data on its interaction with biotin, and a monomeric version called mSA2<SUP>6</SUP> because we feared that the tetrameric streptavidin would cause agglutination of our Cerberus protein. In case we needed to release the streptavidin linked to our function into the surrounding medium, we also included a TEV-protease site to cut off this section.</p> | ||
| − | <p>By adding a 15-residue AviTag, we managed to biotinylate our proteins with the help of BirA<SUP> | + | <p>By adding a 15-residue AviTag, we managed to biotinylate our proteins with the help of BirA<SUP>2</SUP>. For this in-vivo biotinylation, we have transformed our chassis with a plasmid containing the protein BirA.</p> |
| − | + | <h3>References</h3> | |
| + | |||
| + | <i> | ||
| + | <ol style=" font-size:15px;"> | ||
| + | <li> E.S. Nogueira et al. / Protein Expression and Purification 93 (2014) 54–62 | ||
| + | <li> K. H. Lim, H. Huang, A. Pralle, et S. Park, « Stable, high-affinity streptavidin monomer for protein labeling and monovalent biotin detection », Biotechnol. Bioeng., vol. 110, no 1, p. 57-67, janv. 2013. | ||
| + | </ol> | ||
| + | </i> | ||
</div> | </div> | ||
| Line 130: | Line 156: | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
Revision as of 16:44, 12 October 2018
DESCRIPTION
Cellulose: a Material with Endless Possibilities
With approximatively fifty billion tonnes produced yearly, cellulose is the most abundant bio-polymers on earth. Cellulose is a linear polysaccharide of D-glucose residues linked to each other via β-1,4 bonds. It is mainly synthetized in the plant cell wall, associated with other molecules, in order to shape plant body. However, cellulose is also secreted in the surrounding of aerobic bacteria such as Gluconacetobacter hansenii in order to form a bio-film enabling oxygen uptake. Nowadays, cellulose and its derivatives (nitrocellulose, cellulose acetate, methyl cellulose, carboxymethyl cellulose, etc…) are among the first materials that have been intensively used in industries (wood, cotton, textiles, paper, electronics and biomedical devices1), representing a market size evaluated at USD 20.61 billion in 2015.
Bacterial cellulose has also been the target of the research and development in industries. As it is naturally purer than plant cellulose, it doesn’t need to go through harsh purification processes that cost a lot of energy, time and money2>/sup>. However, different types of cellulose with various properties and degrees of purity are used in the industry, which explains the advantage of having a system that could manage with different type of cellulose.
By functionalising cellulose, we aim to demonstrate how this widely used material can be more than a simple packaging or textile fibres. By combining it to our protein platform Cerberus, cellulose can become a source of information and bring new opportunities for industrial applications.
References
- Keshk SM: Bacterial Cellulose Production and its Industrial Applications. Journal of Bioprocessing & Biotechniques 2014, 4;2. DOI: 10.4172/2155-9821.1000150.
- Faezah Esa SMT, Norliza Abd Rahman: Overview of Bacterial Cellulose Production and Application. Agriculture and Agricultural Science Procedia 2 2104:113-119. DOI: 10.1016/j.aaspro.2014.11.017.
- Serge Perez, (2000), Structure et morphologie de la cellulose.
- Keshk SMAS (2014) Bacterial Cellulose Production and its Industrial Applications. J Bioprocess Biotech 4: 150 doi: 10.4172/2155-9821.1000150
- « Overview of Bacterial Cellulose Production and Application », Agric. Agric. Sci. Procedia, vol. 2, p. 113-119, janv. 2014.
Genesis of our project, Cerberus
When brainstorming about the project, we had these different ideas and they all revolved around functionalising several materials. We then realised it could be of great use to have one material that we could functionalise at our discretion. That is how we decided to work on cellulose, especially bacterial cellulose, in hope of developing its use by adding a whole range of exciting possibilities. From conductive paper to anti-infection tissues, applications domains are aplenty (medicine, textile, stationery, etc). The major bottleneck is the complexity to conjugate bioactive molecules to cellulose.
To circumvent this limitation and enable a wide range of chemicals to be fixated to cellulose, we designed a three headed linker protein named Cerberus (in reference to the mythological dog). Cerberus is based on the fusion of three fixating protein structures representing the three heads of the system. The first head is a protein domain of the type 3 Carbohydrate Binding Module (CBM3) family to bind cellulose. The second is one of the strongest linkage systems of the living realm, streptavidin, with its high affinity for biotinylated compounds. The last of the heads features a non-natural amino acid, 4-L-azidophenylalanine, catalysing covalent bonds by click chemistry. Therefore, the versatility of our thought-out linker will allow a large variety of organic and inorganic molecules to conjugate with cellulose.
One head to bind to cellulose, the CBM3a
The first head is the core of our linker, Cerberus. We chose the Carbohydrate Binding Module type 3a (CBM3a) to bind to cellulose. This domain is found in the cellulosome of Clostridium thermocellum1 and its four aromatic amino acids make it the perfect candidate to bind to cellulose through a dipole-dipole interaction between the CBM3a’s aromatic amino acids and the cellulose’s glucose rings.
Our CBM3a features a long endogenous linker on each end, to which we can attach other structures to functionalise cellulose.
References
- E. Morag et al., « Expression, purification, and characterization of the cellulose-binding domain of the scaffoldin subunit from the cellulosome of Clostridium thermocellum. », Appl. Environ. Microbiol., vol. 61, no 5, p. 1980-1986, mai 1995.
One head to bind biological macromolecules, streptavidin
The second head of Cerberus is streptavidin, which has been added to cellulose N-Terminus. Streptavidin is a 60 kDa homotetrameric protein, isolated from Streptomyces avidinii, and it is well known for its interaction with biotin and biotinylated proteins. With a dissociation constant of 10-13 M, the interaction between streptavidin and biotin is the strongest non-covalent one known in Nature5.
The sequence of streptavidin wild type is used in fusion with the CBM3a. This streptavidin forms a complex with three other streptavidin monomers, hence the unmatched affinity for biotin since it can bind four molecules of biotin per tetramer. We decided to use two versions of streptavidin: the native form which is tetrameric because we have data on its interaction with biotin, and a monomeric version called mSA26 because we feared that the tetrameric streptavidin would cause agglutination of our Cerberus protein. In case we needed to release the streptavidin linked to our function into the surrounding medium, we also included a TEV-protease site to cut off this section.
By adding a 15-residue AviTag, we managed to biotinylate our proteins with the help of BirA2. For this in-vivo biotinylation, we have transformed our chassis with a plasmid containing the protein BirA.
References
- E.S. Nogueira et al. / Protein Expression and Purification 93 (2014) 54–62
- K. H. Lim, H. Huang, A. Pralle, et S. Park, « Stable, high-affinity streptavidin monomer for protein labeling and monovalent biotin detection », Biotechnol. Bioeng., vol. 110, no 1, p. 57-67, janv. 2013.
One head to bind inorganic molecules, 4-L-azidophenylalanine
To expand the versatility of our system, on the C-Terminus of the CBM3a, an unnatural amino acid called 4-L-azidophenylalanine was added. Its structure is like that of a phenylalanine, except that it presents an azide, or N-three, function on its tip, as the name would suggest. When presented with an alkyne function, and in particular dibenzocyclooctyne (DBCO), a reaction called click chemistry allows us to covalently bond these functions to our Cerberus protein in a spontaneous and irreversible way.
The strategy used to incorporate this unnatural amino acid into our protein is to bring an orthogonal pair of tRNA and aminoacyl-tRNA synthetase with our plasmid8. The tRNA will recognize the amber codon TAG and this codon will not stop the translation as it normally does. Instead, it will allow the incorporation of our unnatural amino acid, the 4-L-azidophenylalanine.
There are two types of click chemistry that can be done on 4-L-azidophenylalanine to functionalise our Cerberus. The first one is the copper-catalyzed azide-alkyne cycloaddition reaction (CuAAC). It takes place as its name suggests between the azide group of the unnatural amino acid and an alkyne group; the reaction is catalysed by Cu2+ ions. The main problem of this method is the cytotoxicity of copper on cells limits its use in assays that take place in the cellular environment. The second type of click is the strain-promoted azide-alkyne cycloaddition reaction (SPAAC) which proceeds without the need of a catalyst9.
For our experimental plan, we decided to use both types of click chemistry, but we managed to only use the SPAAC during our time in the lab.
No dogs were harmed over the course of this iGEM project.
The whole Toulouse INSA-UPS team wants to thank our sponsors, especially:
And many more. For futher information about our sponsors, please consult our Sponsors page.
The content provided on this website is the fruit of the work of the Toulouse INSA-UPS iGEM Team. As a deliverable for the iGEM Competition, it falls under the Creative Commons Attribution 4.0. Thus, all content on this wiki is available under the Creative Commons Attribution 4.0 license (or any later version). For futher information, please consult the official website of Creative Commons.
This website was designed with Bootstrap (4.1.3). Bootstrap is a front-end library of component for html, css and javascript. It relies on both Popper and jQuery. For further information, please consult the official website of Bootstrap.