The ubiquitin-proteasome pathway and synaptic plasticity

Abstract

Proteolysis by the ubiquitin-proteasome pathway (UPP) has emerged as a new molecular mechanism that controls wide-ranging functions in the nervous system, including fine-tuning of synaptic connections during development and synaptic plasticity in the adult organism. In the UPP, attachment of a small protein, ubiquitin, tags the substrates for degradation by a multisubunit complex called the proteasome. Linkage of ubiquitin to protein substrates is highly specific and occurs through a series of well-orchestrated enzymatic steps. The UPP regulates neurotransmitter receptors, protein kinases, synaptic proteins, transcription factors, and other molecules critical for synaptic plasticity. Accumulating evidence indicates that the operation of the UPP in neurons is not homogeneous and is subject to tightly managed local regulation in different neuronal subcompartments. Investigations on both invertebrate and vertebrate model systems have revealed local roles for enzymes that attach ubiquitin to substrate proteins, as well as for enzymes that remove ubiquitin from substrates. The proteasome also has been shown to possess disparate functions in different parts of the neuron. Here I give a broad overview of the role of the UPP in synaptic plasticity and highlight the local roles and regulation of the proteolytic pathway in neurons.

Figure 1.

The ubiquitin-proteasome pathway (UPP). In this proteolytic pathway, ubiquitin (single ubiquitin molecules are represented by open circles with straight tails) is selectively and covalently linked to the substrate. The enzymatic process of attaching ubiquitin to substrates is called ubiquitination or ubiquitin conjugation and depends on the action of three different classes of enzymes, E1, E2, and E3. First, ubiquitin is activated by E1 to form a ubiquitin-AMP intermediate. Activated ubiquitin (closed circles with straight tails) is passed on to E2 (ubiquitin carrier enzymes). E2s transfers ubiquitin to an E3 (ubiquitin ligase), which ligates the activated ubiquitin to the substrate. To the ubiquitin, which is attached to a substrate, another ubiquitin is attached and thus, through successive linkages of ubiquitin, a polyubiquitin chain forms. Polyubiquitinated substrates are degraded by a proteolytic complex called the 26S proteasome in an ATP-dependent reaction. Ubiquitin is not degraded but the polyubiquitin chain is disassembled and ubiquitin is recycled by deubiquitinating enzymes (DUBs). Before being committed to be degraded by the proteasome, ubiquitination is reversible. DUBs can disassemble the polyubiquitin chain if a substrate is ubiquitinated erroneously and prevent the degradation of the substrate. (Figure modified from Hegde 2004 and reprinted with permission from Elsevier © 2004.)

Figure 2.

Classes of ubiquitin ligases (E3s). (I) HECT-domain E3. E6-AP ubiquitin ligase in combination with E6 protein and one of the two E2s (UbcH5 or UbcH7) ligates ubiquitin to the p53 tumor suppressor protein. (IIA) A single-subunit RING finger E3. Mdm2 ligates ubiquitin to PSD-95 with the help of an E2 enzyme. (IIBi) A multisubunit RING finger E3. SCF ligases contain the substrate recognition site on an F-box protein. Skp1 is an adaptor that joins the F-box protein to Cul1. RING finger domain is on Rbx 1. The E2 is Ubc3. Cul 1 is modified by Nedd8, a ubiquitin-like protein leading to an increase in the activity of the ligase complex. The substrate is phosphorylated (diamonds) IκBα. (IIBii) A multisubunit RING finger E3. APC is a more complex example of multisubunit RING finger E3s and has a subunit composition distinct from that of SCF. Cdc20 protein in APC has the substrate (Cyclin) recognition site. The RING finger domain is on APC11. The E2s Ubc 11 or UbcX can function with the APC ligase. In addition, several adaptor proteins, some labeled (Cdc27, Cdc23, APC 1, Cdc16) and some unlabeled, interact with Cdc20 and APC11. Diamonds on the adaptor subunits indicate phosphorylation. The polyubiquitin chain is shown on the substrates in each panel. In all panels, E2s are light blue, RING finger domains are dark blue, and the substrates are purple in color. (Figure modified from Hegde 2004 and reprinted with permission from Elsevier © 2004.)

Figure 3.

Combinatorial coding of specificity in ubiquitin conjugation. Two E1s (indicated by two colors in the center) provide some degree of specificity to an ubiquitination reaction. E2s preferentially interact with some E3s but not others. An E3, which may be a single molecule or a complex of molecules, is believed to be specific for each substrate. E2s, E3s, and substrates generate a large number of combinations to “code” for the specificity of an ubiquitination reaction. The shapes on each concentric circle (from inside to outside) represent specific E2s, E3s, and substrates. The notches or projections in each shape represent specific domains in the enzymes or substrates. Radiating dotted lines indicate shapes that fit into each other, indicating specific interactions. Occasionally, an E2 can interact with more than one E3 and a given E3 can ubiquitinate more than one substrate (wavy arrows between circles). These interactions still are specific because they likely occur through different recognition domains in these molecules. The ubiquitinated proteins can undergo degradation by the proteasome or endocytosis or could have a nonproteolytic role. The polyubiquitin chains that are targeted to the 26S proteasome are Lys-48 linked chains, whereas those that subserve nonproteolytic functions and endocytosis are Lys-63 linked (curvy) chains. Monoubiquitin chains also participate in marking some substrates for endocytosis. (Figure modified from Hegde 2004 and reprinted with permission from Elsevier © 2004.)

Figure 4.

Ubiquitin and endocytosis. Receptors on the plasma membrane undergo monoubiquitination as a result of ligand (e.g., neurotransmitter) binding to them. Ubiquitinated receptors bind to proteins called epsins through a ubiquitin-interacting motif (UIM). The epsins in turn interact with adaptor proteins (adaptin) bound to clathrin-coated pits. Ubiquitination also functions to sort the internalized membrane protein into early endosomes, which directs them to degradation by lysosome via the multivesicular body. If ubiquitin from the endocytosed receptors is removed by a UBP, the receptor recycles back to the membrane. Proteasome inhibitors block endocytotic degradation of some proteins, such as glutamate receptor subunits, indicating a possible role for the proteasome. In several cases, a Lys-63-linked polyubiquitin chain attachment (instead of monoubiquitination) plays a role in endocytosis (not depicted). (Figure modified from Hegde 2004 and reprinted with permission from Elsevier © 2004.)

Figure 5.

Opposing local roles of the proteasome in dendrites and in the nucleus during L-LTP. (Top) Proteasome active: When the proteasome in the dendrites is highly active, protein substrates that positively regulate L-LTP are degraded (broken spheres), and therefore the extent of L-LTP is limited and only normal L-LTP ensues. A retrograde signal is likely transmitted to the nucleus. Proteasome aids the transcription of genes by degrading the CREB repressor ATF4 (broken squares in the nucleus) thus allowing for normal L-LTP maintenance. Transcribed mRNAs (triangles) travel to activated synapses. (Bottom) Proteasome inactive: When the proteasome is inhibited (indicated by crosses on the proteasome), newly synthesized proteins in the dendrites are stabilized (intact spheres) and the L-LTP-inducing stimulation protocols dramatically increase (upward arrow) the early part of L-LTP (Ep-L-LTP). The proteasome inhibition obstructs CREB-mediated transcription by preventing the degradation of transcription repressor ATF4 (intact squares in the nucleus). Proteasome inhibition could also inhibit the generation of the retrograde signal. Therefore, L-LTP is not maintained but decays (downward arrow). It is likely that proteasome inhibition also causes failure of sustained translation because of the stabilization of the translation repressors, which accumulate after the induction of L-LTP, thus contributing to the blockade of the L-LTP maintenance.