Parts image

Engineering

Design, Build, Test, Learn... and Hope!

Overview

Our project takes inspiration from the natural plant defense mechanisms RNA interference (RNAi) to protect sugar beets against the Beet Yellows Virus (BYV)[1]. We aimed to engineer bacterial strains that produce specific precursors of interfering RNAs, long hairpin RNA (lhRNA) against the BYV. In addition, we wanted to protect our RNAs using the viral capsid of the Tobacco Mosaic Virus (TMV)[2], either directly isolated from the virus or produced by engineered bacteria. The engineering decisions were based on published results and empirical findings derived from our laboratory investigations. Within this segment of Wiki, we explain our choices while engineering our solution.

Therefore, our project involved the use of the DBTL (Design, Build, Test and Learn) principle for four main parts:

  • Long hairpin RNA (lhRNA) engineering: with the basic parts targeting the phytoene desaturase of sugar beets (BBa_K5055001), the p21 (BBa_K5055002) and the RNA polymerase (BBa_K5055003) of the BYV.

  • Coat proteins engineering: with the basic (BBa_K5055000) and composite parts (BBa_K5055004) encoding the coat proteins from the TMV.

  • Coat proteins isolation

  • Beet Yellows Virus detection

lhRNA engineering

Coat proteins engineering

Coat proteins isolation

Cycle 1

Design: To isolate the coat proteins from the Tobacco Mosaic Virus (TMV) directly we first wanted to amplify our viruses. To do so, the aim was to mechanically inoculate the TMV in the leaves. Then, our goal was to isolate the virus and its proteins.

Build: Once we received the TMV, we inoculated the TMV in the sugar beet leaves using sand or silicon carbide. We then waited two weeks and performed the protein purification as presented in our protocol.

Test: To check the isolation of the coat proteins, we quantified them using BCA assay and performed a SDS-PAGE electrophoresis to see if we got proteins at the expected size of the TMV coat proteins. We did observe a band at around 17.6 kDA.

Learn: We only saw the band ones, and couldn’t replicate the result. We had several hypothesis about this. This could be due to the fact that the virus did not have the time to replicate enough in the plant leaves, creating not enough coat proteins for us to quantify, or that the inoculation did not work. In addition, the protocol to extract the coat proteins could be improved.

Beet Yellows Virus detection

References

[1] Dubrovina, A. S. & Kiselev, K. V. Exogenous RNAs for Gene Regulation and Plant Resistance. Int. J. Mol. Sci. 20, 2282 (2019).
[2] Yang, J., Zhang, L., Zhang, C. & Lu, Y. Exploration on the expression and assembly of virus-like particles. Biotechnol. Notes 2, 51–58 (2021).
[3] Saunders, K., Thuenemann, E. C., Peyret, H. & Lomonossoff, G. P. The Tobacco Mosaic Virus Origin of Assembly Sequence is Dispensable for Specific Viral RNA Encapsidation but Necessary for Initiating Assembly at a Single Site. J. Mol. Biol. 434, 167873 (2022).
[4] Wetzel, V., Willems, G., Darracq, A., Galein, Y., Liebe, S. & Varrelmann, M. The Beta vulagris-derived resistance gene Rz2 confers broad-spectrum resistance against soilborne sugar beet-infecting viruses from different families by recognizing triple gene block protein 1. Mol. Plant. Path. 22, 829-842 (2012).