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Deciphering the SUMO code in plants

ABSTRACT: Post-translational modification (PTM) events generate proteoforms that orchestrate cell signalling in almost every biological process. The SUMOcode project aims to understand a critically important but understudied PTM in plants, SUMO (Small Ubiquitin-like Modifier). The rules governing specificity and function remain rudimentary for most PTMs, but the plant SUMO system provides a unique possibility to unravel the rules governing SUMOylation, as its core machinery comprises only 33 genes in Arabidopsis, compared with many hundreds for other PTMs. Our central hypothesis is that SUMO specificity is conferred through how cells are primed to respond to different stress signals, the tissue and cellular spatial distribution of SUMO machinery and substrates and control of SUMOylation modification via activation, repression and competition for PTM sites. Given the small numbers of genes involved in SUMOylation, we are in an excellent position to test our hypothesis employing state of the art multi-omics technologies to create the first SUMO Cell Atlas of any organism. Our ultimate goal is to 'enable' researchers and breeders to decipher the SUMO code in plants, enabling them to edit and rewrite the code, to develop crops that are future proofed against ongoing climate instability and change.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE275006 | GEO | 2025/07/21

REPOSITORIES: GEO

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Project description:Post translational protein modifications (PTMs) including small chemical groups and small proteins, belonging to the ubiquitin family, are essential for virtually all cellular processes. In addition to modification by a single PTM, proteins can be modified by a combination of different modifiers, which are able to influence each other. Since little is known about crosstalk between different ubiquitin family members, we developed an improved method enabling identification of co-modified proteins on a system-wide level using mass spectrometry. We focused on the role of crosstalk between SUMO and ubiquitin during proteasomal degradation. Using two complementary approaches, we identified 498 proteins to be significantly co-modified by SUMO and ubiquitin upon MG132 treatment. These targets included many enzymatic components of PTM machinery, involved in SUMOylation and ubiquitylation, but also phosphorylation, methylation and acetylation, revealing a highly complex interconnected network of crosstalk between different PTMs. In addition various other biological processes were found to be significantly enriched within the group of co-modified proteins, including transcription, DNA repair and the cell cycle. Interestingly, the latter group mostly consisted of proteins involved in mitosis, including a subset of chromosome segregation regulators. We hypothesize that group modification by SUMO-targeted ubiquitin ligases regulates the stability of the identified subset of mitotic proteins, which ensures proper chromosome segregation. The mitotic regulators KIF23 and MIS18BP1 were verified to be co-modified by SUMO and ubiquitin upon inhibition of the proteasome and subsequently identified as novel RNF4 targets. Both modifications on MIS18BP1 were observed to increase simultaneously during late mitosis, while the total protein level decreased immediately afterwards. These results confirm the regulation of MIS18BP1 via SUMO-ubiquitin crosstalk during mitosis. Combined, our work highlights extensive crosstalk between SUMO and ubiquitin, providing a resource for further unraveling of SUMO-ubiquitin crosstalk.

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Deciphering the SUMO code in plants

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