Projets iGEM 2024

PANCE-EVO.T7

iGEM Evry Paris-Saclay

The aim of our project is to develop a powerful directed evolution tool by combining the PANCE technology (Phage-Assisted Non-Continuous Evolution) which allow directed evolution with a self-selecting screening of the best variants and the Evolution.T7 tool developed by the iGEM Evry Paris-Saclay 2021 team  which allows targeted mutagenesis on a specific gene of interest.

The PANCE technology is very useful to avoid a long and fastidious step of screening but the evolution part relies on random mutagenesis on the whole system and not only on our gene of interest. It can result in loss of interesting variants if the system becomes non-functional due to mutations in essential genes.

In contrast, Evolution.T7 only mutates on a specific gene sequence but does not have an auto-screening method such as PANCE.

By combining these two methods in PANCE-EVO.T7, we aim to fasten and improve the discovery of new interesting variants without losing some because of mutations that disrupt the system.

In parallel, we aim to compare the efficiency of the PANCE-EVO.T7 system to find the best variants of a protein and the ability of an AI based model to find such variants. We could resume it as “ Who is the best engineer between nature and AI ? “

Our project will first focus on the evolution of a transcription factor, XylS, recently engineered to detect plastic degradation metabolites. This mutated XylS could then be used to characterize the activity of plastic degradation enzymes, solving a lack of efficient detection  system for their activity. It could also be used to detect small quantities of plastic pollution in water, where our actual techniques cannot detect plastic particles inferior to 100 nm.

Finally, our new directed evolution system and model (we will see who is the best) could be applied to many other biological topics and fields that involve proteins.

Project Morpheus: Synthetising Vanilla through PET upcycling

iGEM Sorbonne

Our project consists of bioremediating water from PET microplastics using Chlamydomonas reinhardtii. This degradation will be performed by enzymatic digestion of PET particles with a triple-fusion split protein system. Following the digestion, the final product will be transformed into high-value molecules, such as terpenes for the cosmetic industry or medicament precursors.

Biopesticides for sugar beet’s preservation

iGEM Ionis

Beta vulgaris, or Sugar beet, accounts for 25% of the sugar in the world, with France being the second-biggest producer [1]. The aphids Myzus persicae and Aphis fabae are the most threatening pests toward B. vulgaris. They can resist most pesticides and are the main vectors for the Beet Yellow Virus (BYV) [2]. More than a third of the crops are affected yearly, and infected plants suffer a yield loss that can reach 50%, which is why farmers are wary of these pests [3].
Neonicotinoids (NEOs) appear as the sole pesticides able to repel efficiently the aphids to protect the crops [3]. As a result, in 2016, almost the totality of sugar beet seeds was undergoing preventive treatment with NEOs [4]. However, in 2018 it was confirmed that this pesticide had adverse effects on human and pollinators health [5]. However, their usage was not totally restricted in the EU until 2023, as years of derogation were granted especially for sugar beets [6]. Now deprived of their most efficient defense, European beets and farmers are more vulnerable to pests. To face this crisis our project was launched.
Small interfering RNAs (siRNA) are one of natural self-defense mechanisms to fight against pathogens (virus, fungi, …). These sequences of around 20 nucleotides target and destroy RNAs, including pathogenic viral RNAs [7]. Using synthetic biology, we engineer the precursors of siRNA (shRNA) to target specific sequences of the BYV. In addition, we hijack the properties of the Tobacco Mosaic Virus’ (TMV) capsid and turn it over to produce artificial and non-pathogenic viral particles. Our idea is to instrumentalize the penetrating and protective properties of the TMV capsid to deliver our shRNA directly to the plants.
Our approach for managing plant viruses using synthetic biology does not involve any genetic modification of the plant. In addition, residues of our product are extremely specific and biodegradable in 48 hours [8]. As a result, they are harmless for all living beings [9].

[1] Hossain R, Menzel W, Lachmann C, Varrelmann M. New insights into virus yellows distribution inEurope and effects of beet yellows virus, beet mild yellowing virus, and beet chlorosis viruson sugar beet yield following field inoculation. Plant Pathol. 2021;70(3):584-593.doi:10.1111/ppa.13306
[2] Margaritopoulos JT, Kati AN, Voudouris CC, Skouras PJ, Tsitsipis JA. Long-term studies on the evolutionof resistance of Myzus persicae (Hemiptera: Aphididae) to insecticides in Greece. Bull Entomol Res.2021;111(1):1-16. doi:10.1017/S0007485320000334
[3] Grimmer MK, Bean KMR, Qi A, Stevens M,Asher MJC. The action of three Beet yellows virus resistance QTLs depends on alleles ata novel genetic locus that controls symptom development. Plant Breed.2008;127(4):391-397. doi:10.1111/j.1439-0523.2008.01515.x
[4] Hauer M, Hansen AL, Manderyck B, et al. Neonicotinoids in sugar beet cultivation in Centraland Northern Europe: Efficacy and environmental impact of neonicotinoid seed treatments andalternative measures. Crop Prot. 2017;93:132-142. doi:10.1016/j.cropro.2016.11.034
[5]Zhang D, Lu S. Human exposure to neonicotinoids and the associated health risks: A review. EnvironInt. 2022 May;163:107201. doi: 10.1016/j.envint.2022.107201. Epub 2022 Mar 25. PMID: 35344909.
[6] Zhang D, Lu S. Human exposure to neonicotinoids and the associated health risks: A review. EnvironInt. 2022;163(March):107201. doi:10.1016/j.envint.2022.107201
[7] Zhan J, Meyers BC. PlantSmall RNAs: Their Biogenesis, Regulatory Roles, and Functions. Annu Rev Plant Biol. 2023;74:21-51. doi:10.1146/annurev-arplant-070122-035226
[8]Dubelman S, Fischer J, Zapata F, et al. Environmental fate of double-stranded RNA inagricultural soils. PLoS One. 2014;9(3):1-7. doi:10.1371/journal.pone.0093155
[9]Dubrovina AS, Kiselev K V. Exogenous RNAs for gene regulation and plant resistance. Int J Mol Sci.2019;20(9). doi:10.3390/ijms20092282