Neuronal SUMOylation: mechanisms, physiology, and roles in neuronal dysfunction

Abstract

Protein SUMOylation is a critically important posttranslational protein modification that participates in nearly all aspects of cellular physiology. In the nearly 20 years since its discovery, SUMOylation has emerged as a major regulator of nuclear function, and more recently, it has become clear that SUMOylation has key roles in the regulation of protein trafficking and function outside of the nucleus. In neurons, SUMOylation participates in cellular processes ranging from neuronal differentiation and control of synapse formation to regulation of synaptic transmission and cell survival. It is a highly dynamic and usually transient modification that enhances or hinders interactions between proteins, and its consequences are extremely diverse. Hundreds of different proteins are SUMO substrates, and dysfunction of protein SUMOylation is implicated in a many different diseases. Here we briefly outline core aspects of the SUMO system and provide a detailed overview of the current understanding of the roles of SUMOylation in healthy and diseased neurons.

FIGURE 1.

The SUMO pathway. All SUMO proteins are first synthesized as inactive precursors that are cleaved by SUMO proteases (SENPs) to reveal mature (conjugatable) SUMO. SUMO is then activated in an ATP-dependent step by the E1 enzyme, a heterodimer of the subunits SAE1 and SAE2. SUMO is then passed to the active site cysteine of the sole SUMO conjugating enzyme, Ubc9, which, in combination with one of a growing number of described E3 enzymes, mediates target recognition and conjugation of SUMO to a lysine residue in the substrate protein. Broadly speaking, SUMOylation can have 4 nonmutually exclusive consequences: the attached SUMO can change the interaction profile of the substrate, either by blocking binding of an interacting protein, or by the attached SUMO acting as a recruitment factor for new proteins. Alternatively, SUMOylation can control substrate stability, through SUMO chain-mediated recruitment of SUMO-targeted ubiquitin ligases (STUbLs), or regulate substrate activity, through inducing a change in protein conformation.

FIGURE 2.

Properties of SUMO1 and SUMO2/3 conjugation. Schematic highlighting the main differences between SUMO1 and SUMO2/3 modification. A: SUMO1 is conjugated to substrates via Ubc9 and cleaved mostly by SENP1/2. SUMO1 does not contain an internal SUMOylation site and therefore cannot form polySUMO chains. B: SUMO2/3 is conjugated by Ubc9 and cleaved by SENP3 or SENP5. Since SUMO2/3 contains SUMOylation sites, SUMO2/3 can form polySUMO chains of n length. SUMO chains are shortened by cleavage by SENP6/7. Conjugation of SUMO1 to SUMO2/3 can cap SUMO2/3 chains to terminate further elongation.

FIGURE 3.

Regulation of SUMO-SIM interactions. SIM-containing proteins mediate the downstream effects of SUMOylation through binding to the SUMOylated substrate. Furthermore, SIMs are present in several components of the SUMOylation machinery, where they act to coordinate substrate SUMOylation. Intriguingly, SUMO-SIM interactions can be reciprocally regulated. A: phosphorylation of the SIM in the E3 ligase PIAS1 by casein kinase 2 (CK2) enhances its capacity to bind SUMO. B: acetylation of SUMO within the SIM-binding groove, which is reversed by class I histone deacetylases (HDACs), blocks SUMO-SIM interactions.

FIGURE 4.

Interplay between substrate SUMOylation and phosphorylation. A: phosphorylation of some substrates, such as MEF2A and GATA-1, promotes SUMOylation via enhaced recruitment of Ubc9. This is due to the negative charge of the phosphate group interacting with a cognate basic patch on Ubc9. Other substrates, such as Elk-1, are efficiently modified by SUMO due to the presence of a negatively charged region immediately COOH-terminal to the modified lysine, mimicking the effect of phosphorylation, a motif known as an NDSM (negatively charged SUMOylation motif). B: conversely, phosphorylation can also reduce SUMOylation of some substrates. For example, phosphorylation of SATB1 reduces its SUMOylation through blocking binding to the E3, PIAS1.

FIGURE 5.

Posttranslational regulation of Ubc9 can alter global SUMOylation, or modification of particular subsets of proteins. A: SUMOylation of some target proteins, such as USP25 and BLM, is enhanced by the presence of a SIM in the substrate, which recruits SUMO-loaded Ubc9 through noncovalent binding to SUMO. However, Ubc9 can also be covalently modified by SUMO at lysine-14, and SUMOylation of Ubc9 acts to enhance its activity towards a subset of SIM-containing proteins, presumably due the covalently attached SUMO promoting recruitment to the substrate. B: phosphorylation of Ubc9 at serine-71 by the kinase Cdk1 enhances its activity in vitro. C: acetylation of Ubc9 at lysine-65 specifically reduces its activity towards NDSM-containing substrates. However, hypoxia results in SIRT1-mediated deacetylation of this residue, enhancing SUMOylation.

FIGURE 6.

The roles of protein SUMOylation at the presynapse. Schematic highlighting proteins involved in key stages of presynaptic vesicle exocytosis. A: the reserve pool of synaptic vesicles is tethered to the actin cytoskeleton by synapsin proteins. On depolarization, calcium influx activates protein kinases, e.g., CaMKII and PKA, which phosphorylate synapsins allowing migration of vesicles from the reserve to the recycling pool. B: vesicles in the recycling pool are docked and primed for release. This process involves many proteins including the SNARE complex (VAMP2, SNAP-25, and syntaxin-1A), munc18a, synaptotagmins, munc13–1, and RIM1α. C: calcium influx through voltage-gated Ca_V channels (clustered by RIM1α) triggers exocytosis of neurotransmitter by binding to synaptotagmin. D: collapsin response mediator protein 2 (CRMP2) is reported to be SUMOylated in neurons. SUMOylation of CRMP2 has been implicated in inhibition of Ca²⁺ entry through Ca_V2.2 channels, and increasing surface expression of Na_V1.7 channels. Named proteins are potential or confirmed SUMO substrates. For confirmed SUMO substrates, the role of SUMOylation is shown, i.e., SUMOylation of RIM1α is required to cluster Ca_V channels and allow coordinated Ca²⁺ entry, and GluK2 SUMOylation triggers kainate receptor endocytosis.

FIGURE 7.

SUMOylation at the postsynapse. SUMOylation regulates postsynaptic structure and function through modification of multiple substrates. A: agonist activation of the kainate receptor (KAR) leads to PKC-mediated phosphorylation and SUMOylation of the GluK2 receptor subunit, ultimately resulting in KAR endocytosis. Although not direct targets themselves, SUMOylation also regulates the trafficking of AMPA receptors. Induction of LTP with the NMDAR coagonist glycine recruits Ubc9 and SUMO to the postsynapse, and SUMOylation is essential for AMPAR insertion into the postsynaptic membrane. Suppression of synaptic activity by TTX blockade of voltage-gated sodium channels causes increased AMPAR insertion and synaptic upscaling. This treatment also causes the loss of the SUMO protease SENP1, promoting SUMOylation of the synaptic protein Arc, which in turn reduces AMPAR endocytosis, resulting in increased AMPAR surface expression. B: SUMOylation modulates neuronal excitability through modification of the potassium channels K2P1 and Kv1.5, and potentially regulates the ability of synapses to meet energy demands through modification of the mitochondrial GTPase Drp1, which controls mitochondrial number.

FIGURE 8.

SUMOylation and ischemia. Hypoxia induces the accumulation of unfolded proteins in the ER, resulting in ER stress, which is sensed by the ER-resident kinase PERK. Activation of PERK, through an unknown mechanism, results in lysosomal rupture and release of the protease cathepsin B (CatB) into the cytosol, which mediates degradation of the SUMO2/3-specific SUMO protease SENP3. Loss of SENP3 leads to increased SUMOylation of multiple SUMO2/3 substrates, including the mitochondrial GTPase Drp1. Drp1 is a crucial mediator of mitochondrial fission and pro-apoptotic cytochrome c release. Enhanced SUMOylation of Drp1 during ischemia favors its distribution to the cytosol, where it is unable to stimulate cytochrome c release, promoting cell survival. In addition to stimulating degradation of SENP3, hypoxia also promotes SUMOylation by inducing SIRT1-mediated deacetylation of Ubc9, which enhances its activity against NDSM-containing substrates, and deSUMOylation of the E1 subunit SAE2, which promotes its activity.