Line 71: | Line 71: | ||
<p> The Edinburgh Overgraduate iGEM team will address those challenges by domesticating the desired host strains, applying synthetic biology (synbio) genetic engineering standards to the design of protein expression and metabolic engineering systems in a number of non-model organisms and characterising the behaviour of these standardised systems in a number of host strains with high potential for industrial applications. Furthermore, although it has its limitations in bacteria, we will include the CRISPR-Cas9 platform to assess its utility in these organisms as it is a potentially useful tool to have a better control of genomic perturbations and maximise those optimal expression systems and metabolic pathways. Through our project, the path is being paved so that other participants in the synbio community will more easily access these organisms in the laboratory, accelerating the understanding of these organisms and increasing the list of strains that are suitable for the manufacture of relevant products, including those that address global conservation challenges. </p> | <p> The Edinburgh Overgraduate iGEM team will address those challenges by domesticating the desired host strains, applying synthetic biology (synbio) genetic engineering standards to the design of protein expression and metabolic engineering systems in a number of non-model organisms and characterising the behaviour of these standardised systems in a number of host strains with high potential for industrial applications. Furthermore, although it has its limitations in bacteria, we will include the CRISPR-Cas9 platform to assess its utility in these organisms as it is a potentially useful tool to have a better control of genomic perturbations and maximise those optimal expression systems and metabolic pathways. Through our project, the path is being paved so that other participants in the synbio community will more easily access these organisms in the laboratory, accelerating the understanding of these organisms and increasing the list of strains that are suitable for the manufacture of relevant products, including those that address global conservation challenges. </p> | ||
− | + | </div> | |
+ | <div class="col-sm-2"></div> | ||
+ | </div> | ||
+ | </div> | ||
+ | </section> | ||
+ | |||
+ | <section id="design"> | ||
+ | <div class="container"> | ||
+ | <div class="row"> | ||
+ | <div class="col-sm-2"></div> | ||
+ | <div class="col-sm-8" style="background-color:white"> | ||
<h2> Design of the Golden Gate Destination Vectors for Transformation in R. jostii </h2> | <h2> Design of the Golden Gate Destination Vectors for Transformation in R. jostii </h2> | ||
<p> We designed a set of Golden Gate destination vectors based on the MoClo standard to enable quick and easy way to create constructs and transformed it to our new Chassis, Rhodococcus jostii RHA1. We chose to use pSRKBB vector (Schmidt-dannert, 2014), which was derived from pSRK21 (Vesely et al., 2003) as the base of these destination vectors. This plasmid contains Corynebacterium replicon (pSR1) and has been successfully transformed to R. erythropolis, a closely related species of R. jostii (Knoppová et al., 2007; Vesely et al., 2003; Archer & Sinskey, 1993). It has also been refined by the removal of illegal sites incompatible with BioBrick standard (Schmidt-dannert, 2014). We removed the illegal sites (BsaI and BbsI) and replace the cloning site of the plasmid with a standard BioBrick cloning site flanked by two verification primer binding site (VF2 and VR), enabling colony PCR for quick screening of insert, derived from pSB1C3. The resulting vector (pSRKM_Empty) can be used as the template to make Level-1 destination vectors by digestion and ligation of standardized LacZα reporter flanked by fusion sites as described in Iverson et al. (2016). | <p> We designed a set of Golden Gate destination vectors based on the MoClo standard to enable quick and easy way to create constructs and transformed it to our new Chassis, Rhodococcus jostii RHA1. We chose to use pSRKBB vector (Schmidt-dannert, 2014), which was derived from pSRK21 (Vesely et al., 2003) as the base of these destination vectors. This plasmid contains Corynebacterium replicon (pSR1) and has been successfully transformed to R. erythropolis, a closely related species of R. jostii (Knoppová et al., 2007; Vesely et al., 2003; Archer & Sinskey, 1993). It has also been refined by the removal of illegal sites incompatible with BioBrick standard (Schmidt-dannert, 2014). We removed the illegal sites (BsaI and BbsI) and replace the cloning site of the plasmid with a standard BioBrick cloning site flanked by two verification primer binding site (VF2 and VR), enabling colony PCR for quick screening of insert, derived from pSB1C3. The resulting vector (pSRKM_Empty) can be used as the template to make Level-1 destination vectors by digestion and ligation of standardized LacZα reporter flanked by fusion sites as described in Iverson et al. (2016). | ||
Line 82: | Line 92: | ||
<h2> References </h2> | <h2> References </h2> | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
<!-- | <!-- | ||
Line 167: | Line 168: | ||
<p>[13] Spaeth, K. (2011). Polychlorinated Biphenyls, 126(4), 217–218. http://doi.org/10.17226/19865 </p> | <p>[13] Spaeth, K. (2011). Polychlorinated Biphenyls, 126(4), 217–218. http://doi.org/10.17226/19865 </p> | ||
<p>[14] Recio-Vega, R., Velazco-Rodriguez, V., Ocampo-G??mez, G., Hernandez-Gonzalez, S., Ruiz-Flores, P., & Lopez-Marquez, F. (2011). Serum levels of polychlorinated biphenyls in Mexican women and breast cancer risk. Journal of Applied Toxicology, 31(3), 270–278. http://doi.org/10.1002/jat.1672 </p> | <p>[14] Recio-Vega, R., Velazco-Rodriguez, V., Ocampo-G??mez, G., Hernandez-Gonzalez, S., Ruiz-Flores, P., & Lopez-Marquez, F. (2011). Serum levels of polychlorinated biphenyls in Mexican women and breast cancer risk. Journal of Applied Toxicology, 31(3), 270–278. http://doi.org/10.1002/jat.1672 </p> | ||
− | + | --><p> Archer, J. A. & Sinskey, A. J. 1993. The DNA sequence and minimal replicon of the Corynebacterium glutamicum plasmid pSR1: evidence of a common ancestry with plasmids from C. diphtheriae. J Gen Microbiol, 139, 1753-9. </p> | |
+ | |||
+ | <p> Iverson, S. V., Haddock, T. L., Beal, J. & Densmore, D. M. 2016. CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enable Rapid Combinatorial Design for Synthetic and Traditional Biology. ACS Synthetic Biology, 5, 99-103. </p> | ||
+ | |||
+ | <p> Knoppová, M., Phensaijai, M., Veselý, M., Zemanová, M., Nešvera, J. & Pátek, M. 2007. Plasmid Vectors for Testing In Vivo Promoter Activities in Corynebacterium glutamicum and Rhodococcus erythropolis. Current Microbiology, 55, 234-239. </p> | ||
+ | |||
+ | <p> Schmidt-dannert, C. 2014. pSRKBB-empty (Plasmid #59449). www.addgene.org. </p> | ||
+ | |||
+ | <p> Vesely, M., Patek, M., Nesvera, J., Cejkova, A., Masak, J. & Jirku, V. 2003. Host-vector system for phenol-degrading | ||
+ | Rhodococcus erythropolis based on Corynebacterium plasmids. Appl Microbiol Biotechnol, 61, 523-7. </p> | ||
+ | <br> | ||
</div> | </div> | ||
</div> | </div> |
Revision as of 16:10, 19 October 2016
-->