Mechanisms, regulation and consequences of protein SUMOylation

Abstract

The post-translational modification SUMOylation is a major regulator of protein function that plays an important role in a wide range of cellular processes. SUMOylation involves the covalent attachment of a member of the SUMO (small ubiquitin-like modifier) family of proteins to lysine residues in specific target proteins via an enzymatic cascade analogous to, but distinct from, the ubiquitination pathway. There are four SUMO paralogues and an increasing number of proteins are being identified as SUMO substrates. However, in many cases little is known about how SUMOylation of these targets is regulated. Compared with the ubiquitination pathway, relatively few components of the conjugation machinery have been described and the processes that specify individual SUMO paralogue conjugation to defined substrate proteins are an active area of research. In the present review, we briefly describe the SUMOylation pathway and present an overview of the recent findings that are beginning to identify some of the mechanisms that regulate protein SUMOylation.

Figure 1. SUMO family proteins

The alignment shows the sequences of human ubiquitin, SUMO-1, SUMO-2, SUMO-3, SUMO-4, Smt3 (Smt3p) and Pmt3 (Pmt3p). Residues identical in all proteins are shown on a cyan background, and include the C-terminal di-glycine motif required for conjugation to substrate proteins (bold). Residues showing only conservative changes across all four proteins are shown in on a pink background and residues showing semi-conservative changes among each of the proteins are shown on a yellow background. Sequence alignment and determination of conservation was performed using the ClustalW program.

Figure 2. SUMO conjugation

SUMO is transcribed as an inactive precursor, which is cleaved by members of the SENP family to expose a C-terminal di-glycine motif (1). This mature form of SUMO is then activated by the ATP-dependent formation of a thioester bond with the active site of the E1 enzyme, a heterodimer of SAE1 and SAE2 (2). The activated SUMO is then passed to the active site cysteine of the E2 conjugating enzyme, Ubc9 (3), which then catalyses the transfer of SUMO to the target protein, often in conjunction with an E3 enzyme (4,5). The SUMOylated substrate displays phenotypic differences to the unmodified form. DeSUMOylation is mediated by SENP family proteases (6). This releases the unmodified target protein (not shown), and mature SUMO, which is then available to undergo further rounds of conjugation to target proteins.

Figure 3. Molecular consequences of SUMOylation

SUMOylation can have three non-mutually exclusive consequences on the substrate protein. (A) SUMO modification can inhibit interactions with substrate-interacting proteins via the occlusion of the interaction site. (B) SUMOylation can create a new binding face on the substrate protein that can recruit other binding partners in a SUMOylation-dependent manner. (C) SUMOylation can lead to a change in conformation of the substrate protein, altering its activity or revealing previously masked binding sites.

Figure 4. Complex interplay between SUMOylation and other post-translational modifications

Summary of the cross-regulation between SUMOylation and other post-translational modifications.

Figure 5. Mechanisms of paralogue specificity

(A) The predominant modification by SUMO-1 of RanGAP1 has been reported to be due to the protection of RanGAP1–SUMO-1 from SENP-mediated deSUMOylation through binding of this complex to RanBP2, an interaction which only occurs weakly for RanGAP–SUMO-2, leaving it susceptible to deSUMOylation. (B) Alternatively, a growing number of SUMO substrates have been shown to contain paralogue-specific SIMs, which can mediate their paralogue-specific SUMOylation through non-covalent binding to the SUMO protein, or to SUMO-loaded Ubc9. (C) Paralogue specificity may arise through the paralogue-specific actions of E3 enzymes, such as RanBP2, which appears to preferentially conjugate SUMO-2 to substrate proteins.