Structural analyses of the plant PRT6-UBR box in the Cys-Arg/N-degron pathway and insights into the plant submergence response

Kim, L.; Lin, C.-C.; Lin, T.-J.; Cao, Y.-C.; Chen, M.-C.; Chou, M.-Y.; Lin, W.-H.; Kim, M.; Wu, J.-L.; Shih, M.-C.; Song, H. K.; Ho, M.-C.

doi:10.1101/2022.08.19.504472

bioRxiv · 10.1101/2022.08.19.504472

Structural analyses of the plant PRT6-UBR box in the Cys-Arg/N-degron pathway and insights into the plant submergence response

Kim, L.·Lin, C.-C.·Lin, T.-J.·Cao, Y.-C.·Chen, M.-C.·Chou, M.-Y.·Lin, W.-H.·Kim, M.·Wu, J.-L.·Shih, M.-C.·Song, H. K.·Ho, M.-C.

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Abstract

The submergence response in higher plants is highly dependent on the protein stability of group VII ethylene response factors, which are primarily degraded through the oxygen-dependent Cys-Arg branch of the N-degron pathway of targeted proteolysis. Knockout of PRT6, an E3 ligase and a vital component of the N-degron pathway, improves submergence tolerance in Arabidopsis and barley but is associated with side effects such as germination deficiency. In this study, we determined structures of rice and Arabidopsis PRT6-UBR box in complex with various Arg/N-degron related peptides. We identified two highly conserved motifs in the plant PRT6-UBR box, which is responsible for Cys-Arg/N-degron recognition. Structural and mutagenesis studies revealed the importance of two conserved motifs for Cys-Arg/N-degron recognition. The phenotype of Arabidopsis seedlings with PRT6-UBR mutants in these newly identified conserved motifs showed superior submergence survival suggesting that rational manipulation of the PRT6-UBR box can improve flood tolerance. Our results provide an engineering platform for generating crops with improved submergence tolerance.

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Kim, L., Lin, C.-C., Lin, T.-J., Cao, Y.-C., Chen, M.-C., Chou, M.-Y., Lin, W.-H., Kim, M., Wu, J.-L., Shih, M.-C., Song, H. K., Ho, M.-C.. 2022-08-19. Structural analyses of the plant PRT6-UBR box in the Cys-Arg/N-degron pathway and insights into the plant submergence response. https://doi.org/10.1101/2022.08.19.504472

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