Structural insights into SUMO E1–E2 interactions in Arabidopsis uncovers a distinctive platform for securing SUMO conjugation specificity across evolution

Abstract

SUMOylation of proteins involves the concerted action of the E1-activating enzyme, E2-conjugating enzyme and E3-ligases. An essential discrimination step in the SUMOylation pathway corresponds to the initial interaction between E1 ubiquitin-fold domain (UFD) and E2 enzymes. Although E2 orthologs possess high sequence identity, the E2 binding region of the UFD domains has diverged across evolution. Moreover, in reciprocal in vitro conjugation reactions Arabidopsis E1 and E2 SCE1 fail to interact efficiently with cognate human E2 Ubc9 and E1 partners, respectively. To gain more insights into the properties of this interface in evolutionary distant organisms, we solved the crystal structure of SUMO E2 SCE1 and its complex with E1 UFD in Arabidopsis. In addition to a few common structural determinants, the interface between the E1 UFD and E2 in Arabidopsis is distinct compared with human and yeast, in particular by the presence of a longer α-helix in the Arabidopsis UFD domain. Despite the variability of E1 UFD domains in these surfaces, they establish specific interactions with highly conserved surfaces of their cognate E2 enzymes. Functional analysis of the different E2 interface residues between human and Arabidopsis revealed Val37 (Met36 in human), as a determinant that provides specificity in the E1–E2 recognition in plants.

Revised annotation and extended characterizations of components of the Chlamydomonas reinhardtii SUMOylation system

“…The SCE3 splice variants, SCE3.t1 and SCE3.t2, were included in the modeling. The available Arabidopsis SCE1 model (Liu, Lois, & Reverter, 2019) was used as a template for modeling. The global model quality estimate (GMQE) score with a number between 0 (low) and 1 (high) was used to evaluate the expected accuracy of a built model (Biasini et al., 2014).…”

(De)Activation (Ir)Reversibly or Degradation: Dynamics of Post-Translational Protein Modifications in Plants

“…In a second step, recruitment of the E2-conjugating enzyme to the E1 is facilitated by highspecificity protein-protein interactions that have undergone molecular coevolution. This coevolution has resulted in biochemical incompatibility among heterologous SUMO E1-E2 from evolutionarily distant species [138][139][140]. In this step, SUMO is transferred from the E1 to the E2 through a trans-esterification reaction.…”

SUMOylation in Phytopathogen Interactions: Balancing Invasion and Resistance

“…The SAE2 contains an additional domain, referred as the C-terminal domain, that is a disordered domain responsible for SUMO E1 nuclear localization (Castaño-Miquel et al, 2013;Más et al, 2020). The high specificity identified in E1-E2 interactions, most likely as a result of a coevolution process, highlight the importance of conducting biochemical studies using homologous systems to obtain robust results (Reiter et al, 2013(Reiter et al, , 2016Liu et al, 2017;Liu B. et al, 2019). The loaded E2 is competent to catalyze SUMOylation to the protein target.…”