Paradoxes of Cellular SUMOylation Regulation: A Role of Biomolecular Condensates?

Abstract

Protein SUMOylation is a major post-translational modification essential for maintaining cellular homeostasis. SUMOylation has long been associated with stress responses as a diverse array of cellular stress signals are known to trigger rapid alternations in global protein SUMOylation. In addition, while there are large families of ubiquitination enzymes, all small ubiquitin-like modifiers (SUMOs) are conjugated by a set of enzymatic machinery comprising one heterodimeric SUMO-activating enzyme, a single SUMO-conjugating enzyme, and a small number of SUMO protein ligases and SUMO-specific proteases. How a few SUMOylation enzymes specifically modify thousands of functional targets in response to diverse cellular stresses remains an enigma. Here we review recent progress toward understanding the mechanisms of SUMO regulation, particularly the potential roles of liquid-liquid phase separation/biomolecular condensates in regulating cellular SUMOylation during cellular stresses. In addition, we discuss the role of protein SUMOylation in pathogenesis and the development of novel therapeutics targeting SUMOylation. SIGNIFICANCE STATEMENT: Protein SUMOylation is one of the most prevalent post-translational modifications and plays a vital role in maintaining cellular homeostasis in response to stresses. Protein SUMOylation has been implicated in human pathogenesis, such as cancer, cardiovascular diseases, neurodegeneration, and infection. After more than a quarter century of extensive research, intriguing enigmas remain regarding the mechanism of cellular SUMOylation regulation and the therapeutic potential of targeting SUMOylation.

Fig. 1

The SUMO conjugation/deconjugation cascade. SUMO precursors are first processed by SENPs into mature SUMO before being activated by the SUMO E1-activating enzyme to generate a high-energy SUMO-E1 thioester bond, which is then handed over to the SUMO E2-conjugating enzyme. With the assistance of a SUMO E3 ligase, SUMO E2 transfers the SUMO moiety to the ε-amine of a lysine residue on a target substrate. The SUMOylation cycle is completed by SENP isopeptidases that release the covalently attached SUMO moiety from the substrate.

Fig. 2

Human SUMO isoforms. Sequence alignment of putative human SUMO isoforms, SUMO1 (P63165), SUMO2 (P61956), SUMO3 (P55854), SUMO4 (Q6EEV6), SUMO5 (G2XKQ0), SUMO6 (QFR53058), and ubiquitin. Colored boxes highlight identical amino acid residues.

Fig. 3

Conformational changes in SUMO E1 enzyme associated with the adenylate and thioester intermediate formation half-reactions. Cartoon representation for the SUMO E1 in complex with SUMO1-ATP·Mg²⁺ (A, PDB 1Y8R) or a SUMO1-AMP mimic (B, PDB 3KYC) and SUMO E1∼SUMO1-AMP tetrahedral intermediate mimic (C, PDB 3KYD).

Fig. 4

LLPS and protein SUMOylation work in tandem in biomolecular condensates. (A). Multivalent interactions among SUMOylated proteins and SUMO binding proteins enhance LLPS. (B). LLPS enriches SUMOylation machinery in biomolecular condensates to accelerate cellular SUMOylation. (C). LLPS and protein SUMOylation drive the formation of biomolecular condensates.

Fig. 5

Small-molecule inhibitors of SUMO E1 targeting an allosteric binding site (A) or the ATP binding pocket (B). Cartoon representation for the SUMO E1 in complex with HB007 (A, PDB 6CWY) and an ML-792 analog (B, PDB 6XOI). The catalytic Cyc173 is highlighted in red while Cys30 is colored in blue.