Project (Gregor Bucher)
Pushing the limits of RNAi for pest control
Background: RNAi is an emerging technology for eco-friendly and species-specific pest control. One of the challenges is the identification of the best RNAi target sequences, i.e. those that lead to the death of the target at minimal concentrations and with minimal side effects on other species. The difficulty in performing systematic large-scale screens in pest species has limited the number of genes that have been tested in the past. In a genome wide RNAi screen, we have recently identified the most efficient RNAi target genes in the red flour beetle Tribolium castaneum and have shown that the best processes for RNAi mediated pest control are different from those of classic pesticides: They are mainly basic cellular processes including protein production and degradation.
Now, as the best target genes and processes are known, we strive for enhancing the design of the target dsRNAs itself. You will join an ongoing project, where we study the processing of siRNAs by small RNA sequencing to predict the best siRNAs. Hypotheses with respect to the design of optimal target sequences will be tested by in vivo RNAi and the optimized target designs will be transferred to target several pest beetles. Together with our collaborators, we aim at reaching the level of field tests for several different beetles and fungi.
One key prerequesite for successful pest control by RNAi is the uptake of dsRNA by cells (systemic or environmental RNAi). While the presence of an importer is very likely, the respective receptor protein remains elusive for insects while it is known for nematodes. In the second part of the project, you will use comparative genomics and differential RNA sequencing to predict candidate importers and to test them functionally. To that end, you will apply RNAi and CRISPR/Cas9 genome editing.
The project is part of an international collaborative project funded by the European Union (decision pending) and will include travel to our collaborators in Estonia and other countries.
Techniques:
- small RNA sequencing and analysis
- RNA sequencing and differential expression analysis
- Comparative genomics
- molecular cloning and production of dsRNAs
- RNAi in vivo tests in our lab model system and in real pest species
- genome editing by CRISPR/Cas9
Homepage Research Grouphttp://wwwuser.gwdg.de/~gbucher1/index.html
Buer B, Dönitz J, Milner M, Mehlhorn S, Hinners C, Siemanowski-Hrach J, et al. Superior target genes and pathways for RNAi-mediated pest control revealed by genome-wide analysis in the beetle Tribolium castaneum. Pest Manag Sci. 2024. https://doi.org/10.1002/ps.8505.
Ulrich J, Dao VA, Majumdar U, Schmitt-Engel C, Schwirz J, Schultheis D, et al. Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target. BMC Genomics. 2015;16.
Schmitt-Engel C, Schultheis D, Schwirz J, Ströhlein N, Troelenberg N, Majumdar U, et al. The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology. Nat Commun. 2015;6:7822.
Tomoyasu Y, Miller SC, Tomita S, Schoppmeier M, Grossmann D, Bucher G. Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium. Genome Biol. 2008;9:R10.
Bucher G, Scholten J, Klingler M. Parental RNAi in Tribolium (Coleoptera). Curr Biol. 2002;12:R85–6.
Reviews:
Cedden D, Bucher G. The quest for the best target genes for RNAi-mediated pest control. Insect Mol Biol. 2024. https://doi.org/10.1111/imb.12966.
Mehlhorn S, Hunnekuhl VS, Geibel S, Nauen R, Bucher G. Establishing RNAi for basic research and pest control and identification of the most efficient target genes for pest control: a brief guide. Front Zool. 2021;18:60.