Difference between revisions of "Team:Virginia/Papers"

 
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              <a class="hvr-sweep-to-right" href="index.html#abstract">Abstract</a>
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              <a class="hvr-sweep-to-right" href="#">Inspiration</a>
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              <a class="hvr-sweep-to-right" href="#">Papers</a>
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              <a class="hvr-sweep-to-right" href="#">Nucleic Acids</a>
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                The lack of a versatile and reliable way to improve metabolic flux channeling, pathway orthogonality, and product yields is a major impediment to the expanded utilization of biosynthesis for the production of drugs and industrially valuable chemicals. Manifold, a platform technology that addresses this problem, consists of <div class="dict">bacterial microcompartments<span><img src="https://upload.wikimedia.org/wikipedia/commons/thumb/2/25/Carboxysome_and_bacterial_microcompartments.jpg/800px-Carboxysome_and_bacterial_microcompartments.jpg"/>Bacterial microcompartments (BMCs) are organelle-like structures, consisting of a protein shell that encloses enzymes and other proteins. BMCs are typically about 40–200 nanometers in diameter and are entirely made of proteins. The shell functions like a membrane, as it is selectively permeable.</span></div> (BMCs) with encapsulated dsDNA scaffolds <div class="ref">[1]<span>Elbaz, J., Yin, P., &amp; Voigt, C. A. (2016). Genetic encoding of DNA nanostructures and their self-assembly in living bacteria. Nature communications, 7(1), 1-11.</span></div> that sequester and spatially organize, at fixed concentrations, biosynthetic enzymes presented as zinc-finger fusion proteins. Here we deliver the designs for an E. coli cell capable of synthesizing resveratrol using the Manifold platform. The Manifold platform will help lower costs and expand the applications of chemical biosynthesis. The lack of a versatile and reliable way to improve metabolic flux channeling, pathway orthogonality, and product yields is a major impediment to the expanded utilization of biosynthesis for the production of drugs and industrially valuable chemicals. Manifold, a platform technology that addresses this problem, consists of bacterial microcompartments (BMCs) with encapsulated dsDNA scaffolds that sequester and spatially organize, at fixed concentrations, biosynthetic enzymes presented as zinc-finger fusion proteins. Here we deliver the designs for an E. coli cell capable of synthesizing resveratrol using the Manifold platform. The Manifold platform will help lower costs and expand the applications of chemical biosynthesis.
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              The invention consists of a protein shell comprising one or more proteins, one or more nucleic acid scaffolds of which there can be multiple copies, anabolic and/or catabolic enzymes specific to the desired biosynthesis pathway each containing a nucleic acid binding domain, recognition sequences for the utilized nucleic acid binding domains, nucleic acid spacers, and a linkage between the nucleic acid scaffolds and the protein shell. The protein shell (10) can take the form of any closed or open surface that comprises one or more repeating protein units (12). Examples of valid shells include bacterial microcompartments such as the Pdu, Eut, and carboxysome microcompartments, as well as modified,  but not necessarily closed, surfaces composed of mutated versions of these microcompartment shell proteins. The nucleic acid scaffolds (18) comprise multiple recognition sequences (22) and spacers (32) and can be made from any form of nucleic acid, including: deoxyribonucleic acid, ribonucleic acid, and synthetic nucleic acids such as xeno nucleic acids and peptide nucleic acids among others. These scaffolds are attached to the protein shell. The pathway enzymes are biological proteins whose exact sequences are dependent on the given use case of the invention, but which all contain a nucleic acid binding domain either internal to their structure, or at their N or C terminus.
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              <b>Fig 1.</b> Figure taken from iGEM Tainan 2019 for demo purposes. Notice how the figure is much longer than it is wide, and two images are coupled together to achive this. Try to do that as well so it looks good.
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              Additionally, protein linkers are usually present between this nucleic acid binding domain and the enzyme structure to prevent inhibition of enzyme activity. However the exact linker(s) used,  if any, is(are) also dependent on the specific use case of the invention. These pathway enzymes are attached to the nucleic acid scaffolds via their nucleic acid binding domains. The nucleic acid recognition sequences (22) are unique or semi-unique sequences of nucleic acid monomers on the nucleic acid scaffolds to which the utilized nucleic acid binding domains have some degree of molecular complementarity. These nucleic recognition sequences comprise most of the scaffold and mark the locations to which the DNA binding domains of the pathway enzymes attach to the scaffolds. The nucleic acid spacers (32) are relatively short sequences of nucleic acid monomers that are also present on the nucleic acid scaffolds, between the recognition sequences. The linkage between the nucleic acid scaffolds (18) and protein shell (10) provides a means by which the nucleic acid scaffolds are bound to the protein shell through direct or multi-molecule complementarity. This linkage is found between the nucleic acid scaffolds and the protein shell. One example is through the addition of a nucleic acid binding domain (24) to one or more of the shell proteins forming a nucleic acid binding domain, shell protein fusion (14). Like the pathway enzymes, this nucleic acid binding-domain can be either internal to the shell protein structure or at its N or C terminus, where the exact placement depends on the shell protein being utilized. Alternatively, one or more intermediate proteins can be used to adhere the nucleic acid scaffolds to the shell, where the region of the protein interacting with the shell binds the shell via protein-protein complementarity (28) with a given shell protein, and the region of the protein interacting with the nucleic acid scaffold binds another recognition sequence on the nucleic acid scaffold through another nucleic acid binding domain (30). This forms a shell protein binding, nucleic acid domain fusion (26).<br/><br/><br/>
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            Index:
 
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             <div>General Template Page</div>
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             <div>   Sources</div>
 
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           <div class="sectionTitle" id="Section 1">Section 1</div>
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                 The lack of a versatile and reliable way to improve metabolic flux channeling, pathway orthogonality, and product yields is a major impediment to the expanded utilization of biosynthesis for the production of drugs and industrially valuable chemicals. Manifold, a platform technology that addresses this problem, consists of <div class="dict">bacterial microcompartments<span><img src="https://upload.wikimedia.org/wikipedia/commons/thumb/2/25/Carboxysome_and_bacterial_microcompartments.jpg/800px-Carboxysome_and_bacterial_microcompartments.jpg"/>Bacterial microcompartments (BMCs) are organelle-like structures, consisting of a protein shell that encloses enzymes and other proteins. BMCs are typically about 40–200 nanometers in diameter and are entirely made of proteins. The shell functions like a membrane, as it is selectively permeable.</span></div> (BMCs) with encapsulated dsDNA scaffolds <div class="ref">[1]<span>Elbaz, J., Yin, P., &amp; Voigt, C. A. (2016). Genetic encoding of DNA nanostructures and their self-assembly in living bacteria. Nature communications, 7(1), 1-11.</span></div> that sequester and spatially organize, at fixed concentrations, biosynthetic enzymes presented as zinc-finger fusion proteins. Here we deliver the designs for an E. coli cell capable of synthesizing resveratrol using the Manifold platform. The Manifold platform will help lower costs and expand the applications of chemical biosynthesis. The lack of a versatile and reliable way to improve metabolic flux channeling, pathway orthogonality, and product yields is a major impediment to the expanded utilization of biosynthesis for the production of drugs and industrially valuable chemicals. Manifold, a platform technology that addresses this problem, consists of bacterial microcompartments (BMCs) with encapsulated dsDNA scaffolds that sequester and spatially organize, at fixed concentrations, biosynthetic enzymes presented as zinc-finger fusion proteins. Here we deliver the designs for an E. coli cell capable of synthesizing resveratrol using the Manifold platform. The Manifold platform will help lower costs and expand the applications of chemical biosynthesis.
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                 [1] A. H. Chen and P. A. Silver, “Designing biological compartmentalization,” <i>Trends Cell Biol.</i>, vol. 22, no. 12, pp. 662–670, Dec. 2012, doi: 10.1016/j.tcb.2012.07.002.<br/><br/>
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                [2] A. I. Romero-Pérez, R. M. Lamuela-Raventós, C. Andrés-Lacueva, and M. C. de La Torre-Boronat, “Method for the quantitative extraction of resveratrol and piceid isomers in grape berry skins. Effect of powdery mildew on the stilbene content,” J. Agric. <i>Food Chem.</i>, vol. 49, no. 1, pp. 210–215, 2001.<br/><br/>
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                [3] C. Chowdhury, S. Sinha, S. Chun, T. O. Yeates, and T. A. Bobik, “Diverse Bacterial Microcompartment Organelles,” <i>Microbiol. Mol. Biol. Rev. MMBR</i>, vol. 78, no. 3, pp. 438–468, Sep. 2014, doi: 10.1128/MMBR.00009-14.<br/><br/>
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          <div class="sectionTitle" id="Section 2">Section 2</div>
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                [4] C. Lim, Z. Fowler, T. Hueller, S. Schaffer, and M. Koffas, “High-Yield Resveratrol Production in Engineered Escherichia coli,” <i>Appl. Environ. Microbiol.</i>, vol. 77, pp. 3451–60, Mar. 2011, doi: 10.1128/AEM.02186-10.<br/><br/>
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                [5] C. M. Insights, “Resveratrol Market to Surpass US$ 159.1 Million by 2026 – Coherent Market Insights,” <i>GlobeNewswire News Room</i>, 21-Nov-2018. [Online]. Available: https://www.globenewswire.com/news-release/2018/11/21/1655234/0/en/Resveratrol-Market-to-Surpass-US-159-1-Million-by-2026-Coherent-Market-Insights.html. [Accessed: 27-Oct-2020]<br/><br/>
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                [6] Crowley et al., “Structural Insight into the Mechanisms of Transport across the Salmonella Enterica Pdu Microcompartment Shell.” 2010.<br/><br/>
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                [7] D.-G. Wang, W.-Y. Liu, and G.-T. Chen, “A simple method for the isolation and purification of resveratrol from Polygonum cuspidatum,” <i>Journal of Pharmaceutical Analysis</i>, 10-Dec-2012. [Online]. Available: https://www.sciencedirect.com/science/article/pii/S2095177912001426. [Accessed: 27-Oct-2020]<br/><br/>
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              The invention consists of a protein shell comprising one or more proteins, one or more nucleic acid scaffolds of which there can be multiple copies, anabolic and/or catabolic enzymes specific to the desired biosynthesis pathway each containing a nucleic acid binding domain, recognition sequences for the utilized nucleic acid binding domains, nucleic acid spacers, and a linkage between the nucleic acid scaffolds and the protein shell. The protein shell (10) can take the form of any closed or open surface that comprises one or more repeating protein units (12). Examples of valid shells include bacterial microcompartments such as the Pdu, Eut, and carboxysome microcompartments, as well as modified, but not necessarily closed, surfaces composed of mutated versions of these microcompartment shell proteins. The nucleic acid scaffolds (18) comprise multiple recognition sequences (22) and spacers (32) and can be made from any form of nucleic acid, including: deoxyribonucleic acid, ribonucleic acid, and synthetic nucleic acids such as xeno nucleic acids and peptide nucleic acids among others. These scaffolds are attached to the protein shell. The pathway enzymes are biological proteins whose exact sequences are dependent on the given use case of the invention, but which all contain a nucleic acid binding domain either internal to their structure, or at their N or C terminus.  
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                [8] D.-K. Ro et al., “Production of the antimalarial drug precursor artemisinic acid in engineered yeast,” <i>Nature</i>, vol. 440, no. 7086, pp. 940–943, Apr. 2006, doi: 10.1038/nature04640.<br/><br/>
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                [9] Fan and Bobik, “The N-Terminal Region of the Medium Subunit (PduD) Packages Adenosylcobalamin-Dependent Diol Dehydratase (PduCDE) into the Pdu Microcompartment.”2011.<br/><br/>
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                [10] Garmann, Goldfain, and Manoharan, “Measurements of the Self-Assembly Kinetics of Individual Viral Capsids around Their RNA Genome.” 2009.<br/><br/>
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              <img src="https://static.igem.org/mediawiki/2019/3/31/T--NCKU_Tainan--CBMB-Amplification.png"/>
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                [11] Glazyrina J, Materne EM, Dreher T, Storm D, Junne S, Adams T, Greller G, Neubauer P. "High cell density cultivation and recombinant protein production with Escherichia coli in a rocking-motion-type bioreactor." <i>Microb Cell Fact.</i> 2010 May 30 9: 42. doi: 10.1186/1475-2859-9-42. p.4 left column 5th paragraph<br/><br/>
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                [12] Innovations transforming economies and O. Lives, “The Bio Revolution,” Mckinsey.com. [Online]. Available: https://www.mckinsey.com/~/media/McKinsey/Industries/Pharmaceuticals%20and%20Medical%20Products/Our%20Insights/The%20Bio %20Revolution%20Innovations%20transforming%20economies%20societies%20and%20our%20lives/May_2020_MGI_Bio_Revolution
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              <b>Fig 1.</b> Figure taken from iGEM Tainan 2019 for demo purposes. Notice how the figure is much longer than it is wide, and two images are coupled together to achive this. Try to do that as well so it looks good.
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                _Report.pdf. [Accessed: 27-Oct-2020].<br/><br/>
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                [13] J. B. Parsons et al., “Synthesis of Empty Bacterial Microcompartments, Directed Organelle Protein Incorporation, and Evidence of Filament-Associated Organelle Movement,” <i>Mol. Cell</i>, vol. 38, no. 2, pp. 305–315, Apr. 2010, doi: 10.1016/j.molcel.2010.04.008. [9] T. O. Yeates, J. Jorda, and T. A. Bobik, “The Shells of BMC-Type Microcompartment Organelles in Bacteria,” <i>J. Mol. Microbiol. Biotechnol.</i>, vol. 23, no. 4–5, pp. 290–299, 2013, doi: 10.1159/000351347.<br/><br/>
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                [14] J. Elbaz, P. Yin, and C. A. Voigt, “Genetic encoding of DNA nanostructures and their self-assembly in living bacteria,” <i>Nat. Commun.</i>, vol. 7, no. 1, p. 11179, Apr. 2016, doi: 10.1038/ncomms11179.<br/><br/>
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                [15] Jorda et al., “Exploring Bacterial Organelle Interactomes.” 2015.<br/><br/>
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              Additionally, protein linkers are usually present between this nucleic acid binding domain and the enzyme structure to prevent inhibition of enzyme activity. However the exact linker(s) used,  if any, is(are) also dependent on the specific use case of the invention. These pathway enzymes are attached to the nucleic acid scaffolds via their nucleic acid binding domains. The nucleic acid recognition sequences (22) are unique or semi-unique sequences of nucleic acid monomers on the nucleic acid scaffolds to which the utilized nucleic acid binding domains have some degree of molecular complementarity. These nucleic recognition sequences comprise most of the scaffold and mark the locations to which the DNA binding domains of the pathway enzymes attach to the scaffolds. The nucleic acid spacers (32) are relatively short sequences of nucleic acid monomers that are also present on the nucleic acid scaffolds, between the recognition sequences. The linkage between the nucleic acid scaffolds (18) and protein shell (10) provides a means by which the nucleic acid scaffolds are bound to the protein shell through direct or multi-molecule complementarity. This linkage is found between the nucleic acid scaffolds and the protein shell. One example is through the addition of a nucleic acid binding domain (24) to one or more of the shell proteins forming a nucleic acid binding domain, shell protein fusion (14). Like the pathway enzymes, this nucleic acid binding-domain can be either internal to the shell protein structure or at its N or C terminus, where the exact placement depends on the shell protein being utilized. Alternatively, one or more intermediate proteins can be used to adhere the nucleic acid scaffolds to the shell, where the region of the protein interacting with the shell binds the shell via protein-protein complementarity (28) with a given shell protein, and the region of the protein interacting with the nucleic acid scaffold binds another recognition sequence on the nucleic acid scaffold through another nucleic acid binding domain (30). This forms a shell protein binding, nucleic acid domain fusion (26).<br/><br/><br/>
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                [16] J. Rajawat and G. Jhingan, Chapter 1 - <i>Mass spectroscopy, Data Processing Handbook for Complex Biological Data Sources</i>, pp. 1-20, 2019.<br/><br/>
 +
                [17] Juodeikis et al., “Effect of Metabolosome Encapsulation Peptides on Enzyme Activity, Coaggregation, Incorporation, and Bacterial Microcompartment Formation.” 2020.<br/><br/>
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                [18] Kennedy et al., “Apparent Size and Morphology of Bacterial Microcompartments Varies with Technique.” 2020.<br/><br/>
 +
                [19] M. Gearing, Plasmids 101: Golden Gate Cloning,addgene blog share science. [Online]. Available: https://blog.addgene.org/plasmids-101-golden-gate-cloning. [Accessed: 26-Oct-2020].<br/><br/>
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                [20] M. Katz, H. P. Smits, J. Forster, and J. B. NIELSEN, “Metabolically engineered cells for the production of resveratrol or an oligomeric or glycosidically-bound derivative thereof,” US9404129B2, Aug. 02, 2016.<br/><br/>
 +
                [21] M. Portincaso, A. Gourévitch, S. Gross-Selbeck, and T. Reichert, “How Deep Tech Can Help Shape the New Reality,” <i>BCG Global</i>, 21-Jul-2020. [Online]. Available: https://www.bcg.com/publications/2020/how-deep-tech-can-shape-post-covid-reality. [Accessed: 27-Oct-2020]<br/><br/>
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                [22] M. Samejima and A. Attorney, “Efforts Towards Open Innovation,” Nedo.go.jp. [Online]. Available: https://www.nedo.go.jp/content/100889935.pdf. [Accessed: 27-Oct-2020].<br/><br/>
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                [23] Nature News. [Online]. Available: https://www.nature.com/articles/d42473-020-00220-x. [Accessed: 27-Oct-2020].<br/><br/>
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                [24] Parsons et al., “Synthesis of Empty Bacterial Microcompartments, Directed Organelle Protein Incorporation, and Evidence of Filament-Associated Organelle Movement.” 2010.<br/><br/>
 +
                [25] Q. Wang et al., “Peanut by-products utilization technology,” in <i>Peanuts: Processing Technology and Product Development</i>, Elsevier, 2016, pp. 211–325.<br/><br/>
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                [26] “Resveratrol Market size 2020 industry share, demand, top players, industry size, future growth by 2026,” MarketWatch, 19-Oct-2020. [Online]. Available: https://www.marketwatch.com/press-release/resveratrol-market-size-2020-industry-share-demand-top-players-industry-size-future-growth-by-2026-2020-10-18. [Accessed: 27-Oct-2020].<br/><br/>
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                [27] R. J. Conrado et al., “DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency,” <i>Nucleic Acids Res.</i>, vol. 40, no. 4, pp. 1879–1889, Feb. 2012, doi: 10.1093/nar/gkr888.<br/><br/>
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                [28] Salis, Mirsky, and Voigt, “Automated Design of Synthetic Ribosome Binding Sites to Control Protein Expression.” 2009.<br/><br/>
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                [29] S. D. Axen, O. Erbilgin, and C. A. Kerfeld, “A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method,” <i>PLoS Comput. Biol.</i>, vol. 10, no. 10, Oct. 2014, doi: 10.1371/journal.pcbi.1003898.<br/><br/>
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                [30] Synbiobeta.com. [Online]. Available: https://synbiobeta.com/wp-content/uploads/2018/11/Synbiobeta_Report_8.22.18_Chemicals_v3.pdf. [Accessed: 27-Oct-2020].<br/><br/>
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                [31] “Synthetic biology is shaking up these 5 industries-Some of them might surprise you - SynBioBeta,” Synbiobeta.com, 11-Feb-2020. [Online]. Available: https://synbiobeta.com/synthetic-biology-is-shaking-up-these-5-industries-some-of-them-might-surprise-you/. [Accessed: 27-Oct-2020].<br/><br/>
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                [32] “Team:British Columbia/project/vanillin - 2013.Igem.Org,” Igem.org. [Online]. Available: https://2013.igem.org/Team:British_Columbia/Project/Vanillin. [Accessed: 27-Oct-2020].<br/><br/>
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                [33] T. O. Yeates, C. S. Crowley, and S. Tanaka, “Bacterial Microcompartment Organelles: Protein Shell Structure and Evolution,” <i>Annu. Rev. Biophys.</i>, vol. 39, pp. 185–205, Jun. 2010, doi: 10.1146/annurev.biophys.093008.131418.<br/><br/>
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                [34] Toyeates, English: Stylized view of the carboxysome and related bacterial structures such as the propanediol utilization (Pdu) and ethanolamine utilization (Eut) microcompartments. Distinct hexameric BMC shell proteins carrying out different functions in the shell are shown in different shades of blue. Pentameric vertex proteins are shown in magenta. Encapsulated enzymes are shown in green, organized in layers. [Image: T. Yeates]. 2013.<br/><br/>
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                [35] Waters, <i>Beginners Guide to Liquid Chromatography</i>. [Online]. Available: https://www.waters.com/waters/en_US/HPLC---High-Performance-Liquid-Chromatography-Explained/nav.htm?cid=10048919. [Accessed: 26-Oct-2020].<br/><br/>
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                [36] W. Zha, S. B. Rubin-Pitel, Z. Shao, and H. Zhao, “Improving cellular malonyl-CoA level in Escherichia coli via metabolic engineering,” <i>Metab. Eng.</i>, vol. 11, no. 3, pp. 192–198, May 2009, doi: 10.1016/j.ymben.2009.01.005.<br/><br/>
 +
                [37] Yang et al., “Decoding the Stoichiometric Composition and Organisation of Bacterial Metabolosomes.” 2020.<br/><br/>
 +
                [38] Y. Tsai et al., “Structural Analysis of CsoS1A and the Protein Shell of the Halothiobacillus neapolitanus Carboxysome,” <i>PLoS Biol.</i>, vol. 5, no. 6, Jun. 2007, doi: 10.1371/journal.pbio.0050144.<br/><br/><br/>
 
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[13] J. B. Parsons et al., “Synthesis of Empty Bacterial Microcompartments, Directed Organelle Protein Incorporation, and Evidence of Filament-Associated Organelle Movement,” Mol. Cell, vol. 38, no. 2, pp. 305–315, Apr. 2010, doi: 10.1016/j.molcel.2010.04.008. [9] T. O. Yeates, J. Jorda, and T. A. Bobik, “The Shells of BMC-Type Microcompartment Organelles in Bacteria,” J. Mol. Microbiol. Biotechnol., vol. 23, no. 4–5, pp. 290–299, 2013, doi: 10.1159/000351347.

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[36] W. Zha, S. B. Rubin-Pitel, Z. Shao, and H. Zhao, “Improving cellular malonyl-CoA level in Escherichia coli via metabolic engineering,” Metab. Eng., vol. 11, no. 3, pp. 192–198, May 2009, doi: 10.1016/j.ymben.2009.01.005.

[37] Yang et al., “Decoding the Stoichiometric Composition and Organisation of Bacterial Metabolosomes.” 2020.

[38] Y. Tsai et al., “Structural Analysis of CsoS1A and the Protein Shell of the Halothiobacillus neapolitanus Carboxysome,” PLoS Biol., vol. 5, no. 6, Jun. 2007, doi: 10.1371/journal.pbio.0050144.


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