Difference between revisions of "Team:TU Darmstadt/Project/Biofilm"
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<h1> | <h1> | ||
| − | + | <i>Bacillus subtilis</i> and biofilm formation | |
</h1> | </h1> | ||
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<!----------Insert TEXT Here ---------> | <!----------Insert TEXT Here ---------> | ||
| + | <div class="headline" > | ||
| + | <h4> | ||
| + | <i>Bacillus subtilis</i> | ||
| + | </h4> | ||
| + | </div> | ||
| − | + | <p> | |
| − | + | We aim to convert micropollutants | |
| − | + | in wastewater treatment plants using an | |
| − | + | enzyme-producing biofilm and came to the | |
| − | + | decision that Bacillus subtilis is the best | |
| − | + | choice as our biofilm forming organism. | |
| − | + | </p> | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| + | <p> | ||
| + | <i>Bacillus subtilis</i> is a gram-positive bacterium which is usually found in soil. | ||
| + | Gram-positive bacteria only have one cell membrane and are thus often used for protein secretion.<sup id="cite_ref-1"><a href="#cite_note-1">[1]</a></sup> | ||
| + | On the one hand, secreting proteins is beneficial in protein production because no cell disruption is | ||
| + | necessary to collect the protein and the formation of inclusion bodies can be prevented<sup id="cite_ref-2"><a href="#cite_note-2">[2]</a></sup> . On the | ||
| + | other hand, and in our case specifically, we avoid the issue of bringing enzyme substrates across | ||
| + | the membrane in the cell as well as potential cell toxicity of the substrate and degradation product. | ||
| + | We want to leverage the ability of <i>B. subtilis</i> to secret proteins to immobilize our target enzymes | ||
| + | in the biofilm matrix by fusing them to a matrix protein. This is easier to realize with | ||
| + | <i>B. subtilis</i> as gram-positive model organism than with the gram-negative bacteria, | ||
| + | e.g. <i>Escherichia coli</i>. In addition, <i>B. subtilis</i> is a facultative anaerobic | ||
| + | organism which means it can grow in oxygenic, as well as anaerobic conditions, | ||
| + | which can be of advantage when using the biofilm underwater in the clarifier<sup id="cite_ref-3"><a href="#cite_note-3">[3]</a></sup> . | ||
| + | </p> | ||
| + | <p> | ||
| + | In nature <i>B. subtilis</i> forms biofilms on plant roots as it needs a nutrient source. The | ||
| + | advantage for the plants is that <i>B. subtilis</i> protects it from pathogenic infections by funghi<sup id="cite_ref-4"><a href="#cite_note-4">[4]</a></sup> . | ||
| + | Since <i>B. subtilis</i> is a natural biofilm former, it has been used as model organism | ||
| + | for studying biofilms in the last years<sup id="cite_ref-4"><a href="#cite_note-4">[4]</a></sup> . By using this natural biofilm former, we do not have to | ||
| + | worry about how our organism will form a biofilm. Furthermore, <i>B. subtilis</i> is classified as | ||
| + | generally recognized as safe (GRAS) by the American Food and Drug Administration (FDA)<sup id="cite_ref-5"><a href="#cite_note-5">[5]</a></sup> , unlike other | ||
| + | bacteria which are often pathogenic like <i>E. coli</i> or <i>Staphylococcus aureus</i><sup id="cite_ref-6"><a href="#cite_note-6">[6]</a></sup> . It is very | ||
| + | important for us to use an organism which is generally safe given the fact that we want to bring it | ||
| + | into a wastewater treatment plant. | ||
| + | </p> | ||
| + | <p> | ||
| + | Another characteristic of <i>B. subtilis</i> is its ability to form endospores | ||
| + | when exposed to extreme environmental conditions<sup id="cite_ref-7"><a href="#cite_note-7">[7]</a></sup> . Spores are highly resistant | ||
| + | towards extreme temperature, desiccation, radiation and chemicals. This | ||
| + | resistance makes spores interesting for industrial processes, e.g. by displaying | ||
| + | enzymes on the surface of spores which can then be used in harsh reaction conditions. Furthermore, | ||
| + | they are metabolic inactive but can germinate once nutrients are sufficiently available or when they | ||
| + | experience high pressure<sup id="cite_ref-8"><a href="#cite_note-8">[8]</a></sup> . | ||
| + | </p> | ||
| Line 150: | Line 161: | ||
</div> | </div> | ||
| + | <div class="referencestd"> | ||
| + | <h4 style="text-align: left"> References</h4> | ||
| + | |||
| + | <a class="anchor" id="cite_note-1"></a> | ||
| + | <a class="referencestd" href="https://doi.org/10.1007/s00253-013-4960-4" | ||
| + | target="_blank">1.Liu, L.; Liu, Y.; Shin, H. D. Developing Bacillus Spp. as a Cell Factory for Production of Microbial Enzymes and Industrially Important Biochemicals in the Context of Systems and Synthetic Biology. Applied Microbiology and Biotechnology. Springer July 11, 2013, pp 6113–6127 Doi:10.1007/s00253-013-4960-4 </a> | ||
| + | |||
| + | <a class="anchor" id="cite_note-2"></a> | ||
| + | <a class="referencestd" href="https://doi.org/10.1016/j.bbamcr.2004.02.011" | ||
| + | target="_blank">2.Westers, L.; Westers, H.; Quax, W. J. Bacillus Subtilis as Cell Factory for Pharmaceutical Proteins: A Biotechnological Approach to Optimize the Host Organism. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier November 11, 2004, pp 299–310 Doi:10.1016/j.bbamcr.2004.02.011 </a> | ||
| + | |||
| + | <a class="anchor" id="cite_note-3"></a> | ||
| + | <a class="referencestd" href="https://doi.org/10.1078/0723-2020-00108" | ||
| + | target="_blank">3.Clements, L. D.; Miller, B. S.; Streips, U. N. Comparative Growth Analysis of the Facultative Anaerobes Bacillus Subtilis, Bacillus Licheniformis, and Escherichia Coli. Syst. Appl. Microbiol. 2002, 25 (2), 284–286 Doi:10.1078/0723-2020-00108</a> | ||
| + | |||
| + | <a class="anchor" id="cite_note-4"></a> | ||
| + | <a class="referencestd" href="https://doi.org/10.1038/nrmicro2960" | ||
| + | target="_blank">4. Vlamakis, H.; Chai, Y.; Beauregard, P. Sticking Together: Building a Biofilm the Bacillus Subtilis Way. Nature Reviews Microbiology. NIH Public Access March 2013, pp 157–168 Doi:10.1038/nrmicro2960 </a> | ||
| + | |||
| + | <a class="anchor" id="cite_note-5"></a> | ||
| + | <a class="referencestd" href="https://www.fda.gov/food/generally-recognized-safe-gras/microorganisms-microbial-derived-ingredients-used-food-partial-list" | ||
| + | target="_blank">5. Microorganisms & Microbial-Derived Ingredients Used in Food (Partial List) | FDA https://www.fda.gov/food/generally-recognized-safe-gras/microorganisms-microbial-derived-ingredients-used-food-partial-list (accessed Aug 27, 2020) </a> | ||
| + | |||
| + | <a class="anchor" id="cite_note-6"></a> | ||
| + | <a class="referencestd" href="https://doi.org/10.1093/femsre/fuv015" | ||
| + | target="_blank">6.Hobley, L.; Harkins, C.; MacPhee, C. E. Giving Structure to the Biofilm Matrix: An Overview of Individual Strategies and Emerging Common Themes. FEMS Microbiology Reviews. Oxford University Press June 8, 2015, pp 649–669 Doi:10.1093/femsre/fuv015 </a> | ||
| + | <a class="anchor" id="cite_note-7"></a> | ||
| + | <a class="referencestd" href="https://doi.org/10.1101/2020.08.30.273821" | ||
| + | target="_blank">7. Karava, M.; Gockel, P.; Kabisch, J. Bacillus Subtilis Spore Surface Display of Photodecarboxylase for the Transformation of Lipids to Hydrocarbons. bioRxiv 2020, 2020.08.30.273821 Doi:10.1101/2020.08.30.273821 </a> | ||
| + | <a class="anchor" id="cite_note-8"></a> | ||
| + | <a class="referencestd" href="https://doi.org/10.1128/AEM.71.10.5879-5887.2005" | ||
| + | target="_blank">8.Black, E. P.; Koziol-Dube, K.; Guan, D. Factors Influencing Germination of Bacillus Subtilis Spores via Activation of Nutrient Receptors by High Pressure. Appl. Environ. Microbiol. 2005, 71 (10), 5879–5887 Doi:10.1128/AEM.71.10.5879-5887.2005 </a> | ||
| + | </div> | ||
<!----------Insert TEXT Here ---------> | <!----------Insert TEXT Here ---------> | ||
Revision as of 10:53, 3 October 2020
Bacillus subtilis and biofilm formation
Bacillus subtilis
We aim to convert micropollutants in wastewater treatment plants using an enzyme-producing biofilm and came to the decision that Bacillus subtilis is the best choice as our biofilm forming organism.
Bacillus subtilis is a gram-positive bacterium which is usually found in soil. Gram-positive bacteria only have one cell membrane and are thus often used for protein secretion.[1] On the one hand, secreting proteins is beneficial in protein production because no cell disruption is necessary to collect the protein and the formation of inclusion bodies can be prevented[2] . On the other hand, and in our case specifically, we avoid the issue of bringing enzyme substrates across the membrane in the cell as well as potential cell toxicity of the substrate and degradation product. We want to leverage the ability of B. subtilis to secret proteins to immobilize our target enzymes in the biofilm matrix by fusing them to a matrix protein. This is easier to realize with B. subtilis as gram-positive model organism than with the gram-negative bacteria, e.g. Escherichia coli. In addition, B. subtilis is a facultative anaerobic organism which means it can grow in oxygenic, as well as anaerobic conditions, which can be of advantage when using the biofilm underwater in the clarifier[3] .
In nature B. subtilis forms biofilms on plant roots as it needs a nutrient source. The advantage for the plants is that B. subtilis protects it from pathogenic infections by funghi[4] . Since B. subtilis is a natural biofilm former, it has been used as model organism for studying biofilms in the last years[4] . By using this natural biofilm former, we do not have to worry about how our organism will form a biofilm. Furthermore, B. subtilis is classified as generally recognized as safe (GRAS) by the American Food and Drug Administration (FDA)[5] , unlike other bacteria which are often pathogenic like E. coli or Staphylococcus aureus[6] . It is very important for us to use an organism which is generally safe given the fact that we want to bring it into a wastewater treatment plant.
Another characteristic of B. subtilis is its ability to form endospores when exposed to extreme environmental conditions[7] . Spores are highly resistant towards extreme temperature, desiccation, radiation and chemicals. This resistance makes spores interesting for industrial processes, e.g. by displaying enzymes on the surface of spores which can then be used in harsh reaction conditions. Furthermore, they are metabolic inactive but can germinate once nutrients are sufficiently available or when they experience high pressure[8] .
Experts
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At vero eos et
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et
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Former iGEMers
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Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua.
At vero eos et
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et
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Others
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At vero eos et
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.
References
1.Liu, L.; Liu, Y.; Shin, H. D. Developing Bacillus Spp. as a Cell Factory for Production of Microbial Enzymes and Industrially Important Biochemicals in the Context of Systems and Synthetic Biology. Applied Microbiology and Biotechnology. Springer July 11, 2013, pp 6113–6127 Doi:10.1007/s00253-013-4960-4 2.Westers, L.; Westers, H.; Quax, W. J. Bacillus Subtilis as Cell Factory for Pharmaceutical Proteins: A Biotechnological Approach to Optimize the Host Organism. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier November 11, 2004, pp 299–310 Doi:10.1016/j.bbamcr.2004.02.011 3.Clements, L. D.; Miller, B. S.; Streips, U. N. Comparative Growth Analysis of the Facultative Anaerobes Bacillus Subtilis, Bacillus Licheniformis, and Escherichia Coli. Syst. Appl. Microbiol. 2002, 25 (2), 284–286 Doi:10.1078/0723-2020-00108 4. Vlamakis, H.; Chai, Y.; Beauregard, P. Sticking Together: Building a Biofilm the Bacillus Subtilis Way. Nature Reviews Microbiology. NIH Public Access March 2013, pp 157–168 Doi:10.1038/nrmicro2960 5. Microorganisms & Microbial-Derived Ingredients Used in Food (Partial List) | FDA https://www.fda.gov/food/generally-recognized-safe-gras/microorganisms-microbial-derived-ingredients-used-food-partial-list (accessed Aug 27, 2020) 6.Hobley, L.; Harkins, C.; MacPhee, C. E. Giving Structure to the Biofilm Matrix: An Overview of Individual Strategies and Emerging Common Themes. FEMS Microbiology Reviews. Oxford University Press June 8, 2015, pp 649–669 Doi:10.1093/femsre/fuv015 7. Karava, M.; Gockel, P.; Kabisch, J. Bacillus Subtilis Spore Surface Display of Photodecarboxylase for the Transformation of Lipids to Hydrocarbons. bioRxiv 2020, 2020.08.30.273821 Doi:10.1101/2020.08.30.273821 8.Black, E. P.; Koziol-Dube, K.; Guan, D. Factors Influencing Germination of Bacillus Subtilis Spores via Activation of Nutrient Receptors by High Pressure. Appl. Environ. Microbiol. 2005, 71 (10), 5879–5887 Doi:10.1128/AEM.71.10.5879-5887.2005