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Description

           <img src="" alt="notebook" />
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How & why

                       <img src="" alt="ideonella grafic" />

Our Inspiration

In 2016 a bacterium, Ideonella sakaiensis, was found that is able to use polyethylene terephthalate (PET) as a primary carbon and energy source (Yoshida et al., 2016). This bacterium secrets two different hydrolases into the exterior to execute the first two PET degradation steps (Yoshida et al., 2016). The first hydrolase, PETase, mainly breaks down PET to mono(2-hydroxyethyl) terephtalic acid (MHET). The second hydrolase, the MHETase, then digests MHET to terephthalic acid (TPA) and ethylene glycole (EG). The bacterium itself grows optimally within a pH range of 7-7,5 and a temperature of 30-37°C (Tanasupawat, Takehana, Yoshida, Hiraga, & Oda, 2016). It was also demonstrated that it cannot grow anaerobically and has a GC-rich genome (70,4%) (Tanasupawat et al., 2016; Yoshida et al., 2016). Later in 2018, the PETase was characterized and engineered to improve its performance (Austin et al., 2018).

<img src="" alt="plastic bottle illustration" />

We know that we are not after something completely new. But we want to do this right. so we chose a different organism and tried to tackle obstacles other teams failed to solve.

The iGEM projects that inspired us

Degrading microplastic is not a new idea when it comes to iGEM projects. Similarly inspired by the works of Yoshida and his colleagues (Yoshida et al., 2016) a multitude of different teams have worked on comparable topics. We know that we are not after something completely new. But we wanted to do this right. So we chose a different organism and tried to tackle obstacles other teams failed to solve. Our work was inspired by TJUSLS project on PETase 2016 (1), we are intrigued by the effort Harvard BioDesign 2016 put into their project “Plastikback” (2) and the project of ASIJ Tokyo in 2016 struck the same nerve (3). The approaches by the Teams of Tianjin 2016 (4) and ITB 2017 (5) have gravely encouraged our project as well.

                       <img src="" alt="microplastic icon" />

                       <img src="" alt="chlamy organism" />

Chlamydomonas as a model organism

We propose that combining a photosynthesis active organism with at least the optimized PETase and the MHETase we can create a new way of recycling PET or even degrade PET completely to CO2 and H2O. The organism is then able to use the CO2 coming from the plastic as carbon source. We immediately thought of Chlamydomonas reinhardtii as an organism as it grows fast under energy-efficient conditions.

<img class="check-icon" src=""/> easy to cultivate & phototrophic

<img class="check-icon" src=""/> one organism = single cell

<img class="check-icon" src=""/> well established as model organism

<img class="small-image" src="" alt="chlamy" />

Golden Gate Modular Cloning for Chlamydomonas reinhardtii

To synthesize and assemble all the needed gene constructs to let Chlamydomonas express the PETase and MHETase together with different promotors, terminators, secretion signals, tags and selection markers cloning was done using the Golden Gate Modular Cloning (referred to hereafter as “MoClo”) toolkit for C. reinhardtii (Crozet et al., 2018). The Chlamydomonas MoClo kit is standardized to fit the syntax of the plant synthetic biology community (Patron et al., 2015).

MoClo is an assembly method using type IIS restriction sites first introduced by (Weber, Engler, Gruetzner, Werner, & Marillonnet, 2011). Type IIS restriction enzymes (BpiI; BsaI) cleave outside of their recognition site leaving a four base pair overhang also called a fusion site (Engler, Kandzia, & Marillonnet, 2008). Placing those restriction sites before the 5’ beginning and the 3’ end of a desired DNA fragment in inverse orientation will allow ligation of DNA fragments with compatible fusion sites to be correctly assembled (Weber et al., 2011). Type IIS restriction sites can be constructed to build different overhangs making an assembly of multiple fragments possible (Weber et al., 2011).

                       <img src="" alt="Pverview of the hierarchical and modular cloning system"/>

Fig. 1 Overview of the hierarchical and modular cloning system (Weber et al., 2011). (A) Level 0 plasmid modules containing cloned and sequenced promoters (P), 5′ untranslated regions (U), coding sequences (CDS) and terminators (T). Because of the standardization of the toolkit the desired transcription units can be assembled from selected level 0 plasmids in a one-step digestion and ligation reaction into a level 1 vector. (B) Scheme of a Level 0 (L0) and L1 module. The gene part of a L0 module is flanked by compatible fusion sites providing the correct assembly of these modules when cloned into a L1 destination vector. The fusion sites are four nucleotides long (1-4 and 5-8) and flanked by a BsaI recognition sites.

The MoClo toolkit for Chlamydomonas consists of three different cloning vectors called level 0, 1 and 2. They are used in consecutive assembly steps. Level 0 (referred to hereafter as “L0”) destination vectors contain a selection marker gene such as lacZ or RFP surrounded by two cloning sites (BpiI; BsaI). It is possible to insert gene parts into L0 plasmids such as promotors, coding sequences or UTRs with specific fusion sites and surrounded by BsaI restriction sites (Fig. 1 B). The specific fusion sites and BsaI restriction sites make it possible to correctly assemble those L0 modules onto a next plasmid level 1 (referred to hereafter as “L1”) in one step generating a transcriptional unit (Fig. 1, Tab. 1).

Each assembly is performed in a single reaction mix with the desired insert, the destination vector, DNA ligase and one type IIS restriction enzyme. Correctly assembled L1 modules can then be transformed into C. reinhardtii.

Each L0 module has designated nucleotides as their fusion site determining their cloning position in a L1. The kit offers ten different options for positioning in a L1 plasmid. Those cloning positions for each gene part are defined by its function and altogether its position in a L1 plasmid (Tab. 1).

                       
                           Tab. 1 MoClo L0 to L1 cloning; L1 fusion sites
                           establishing a complete transcriptional unit (TU).
                       
                       <img src="" alt="MoClo L0 to L1 cloning table" />

       </section>

       <section class="width-limit">

Austin, H. P., Allen, M. D., Donohoe, B. S., Rorrer, N. A., Kearns, F. L., Silveira, R. L., . . . Beckham, G. T. (2018). Characterization and engineering of a plastic-degrading aromatic polyesterase. Proceedings of the National Academy of Sciences, 115(19), E4350. Retrieved from http://www.pnas.org/content/115/19/E4350.abstract. doi:10.1073/pnas.1718804115

Crozet, P., Navarro, F. J., Willmund, F., Mehrshahi, P., Bakowski, K., Lauersen, K. J., . . . Lemaire, S. D. (2018). Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas reinhardtii. ACS Synthetic Biology, 7(9), 2074-2086. Retrieved from https://doi.org/10.1021/acssynbio.8b00251. doi:10.1021/acssynbio.8b00251

Engler, C., Kandzia, R., & Marillonnet, S. (2008). A one pot, one step, precision cloning method with high throughput capability. PLOS ONE, 3(11), e3647. doi:10.1371/journal.pone.0003647

Patron, N. J., Orzaez, D., Marillonnet, S., Warzecha, H., Matthewman, C., Youles, M., . . . Haseloff, J. (2015). Standards for plant synthetic biology: a common syntax for exchange of DNA parts. New Phytologist, 208(1), 13-19. Retrieved from https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.13532. doi:10.1111/nph.13532

Purton, S., Szaub, J., Wannathong, T., Young, R., & Economou, C. (2013). Genetic engineering of algal chloroplasts: progress and prospects. Russian Journal of Plant Physiology, 60(4), 491-499.

Tanasupawat, S., Takehana, T., Yoshida, S., Hiraga, K., & Oda, K. (2016). Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly(ethylene terephthalate). Int J Syst Evol Microbiol, 66(8), 2813-2818. doi:10.1099/ijsem.0.001058

Weber, E., Engler, C., Gruetzner, R., Werner, S., & Marillonnet, S. (2011). A Modular Cloning System for Standardized Assembly of Multigene Constructs. PLOS ONE, 6(2), e16765. Retrieved from https://doi.org/10.1371/journal.pone.0016765. doi:10.1371/journal.pone.0016765

Yoshida, S., Hiraga, K., Takehana, T., Taniguchi, I., Yamaji, H., Maeda, Y., . . . Oda, K. (2016). A bacterium that degrades and assimilates poly(ethylene terephthalate). Science, 351(6278), 1196-1199. doi:10.1126/science.aad6359

Weblinks:
1 <a href="https://2016.igem.org/Team:TJUSLS_China/Description" target="blank" rel="noopener"> https://2016.igem.org/Team:TJUSLS_China/Description </a>
2 <a href="https://2016.igem.org/Team:Harvard_BioDesign" target="blank" rel="noopener"> https://2016.igem.org/Team:Harvard_BioDesign </a>
3 <a href="https://2016.igem.org/Team:ASIJ_Tokyo/Results" target="blank" rel="noopener"> https://2016.igem.org/Team:ASIJ_Tokyo/Results </a>
4 <a href="https://2016.igem.org/Team:Tianjin/Description" target="blank" rel="noopener"> https://2016.igem.org/Team:Tianjin/Description </a>
5 <a href="https://2017.igem.org/Team:ITB_Indonesia/Description" target="blank" rel="noopener"> https://2017.igem.org/Team:ITB_Indonesia/Description </a>

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