UEV-1 is an ubiquitin-conjugating enzyme variant that regulates glutamate receptor trafficking in C. elegans neurons

Abstract

The regulation of AMPA-type glutamate receptor (AMPAR) membrane trafficking is a key mechanism by which neurons regulate synaptic strength and plasticity. AMPAR trafficking is modulated through a combination of receptor phosphorylation, ubiquitination, endocytosis, and recycling, yet the factors that mediate these processes are just beginning to be uncovered. Here we identify the ubiquitin-conjugating enzyme variant UEV-1 as a regulator of AMPAR trafficking in vivo. We identified mutations in uev-1 in a genetic screen for mutants with altered trafficking of the AMPAR subunit GLR-1 in C. elegans interneurons. Loss of uev-1 activity results in the accumulation of GLR-1 in elongated accretions in neuron cell bodies and along the ventral cord neurites. Mutants also have a corresponding behavioral defect--a decrease in spontaneous reversals in locomotion--consistent with diminished GLR-1 function. The localization of other synaptic proteins in uev-1-mutant interneurons appears normal, indicating that the GLR-1 trafficking defects are not due to gross deficiencies in synapse formation or overall protein trafficking. We provide evidence that GLR-1 accumulates at RAB-10-containing endosomes in uev-1 mutants, and that receptors arrive at these endosomes independent of clathrin-mediated endocytosis. UEV-1 homologs in other species bind to the ubiquitin-conjugating enzyme Ubc13 to create K63-linked polyubiquitin chains on substrate proteins. We find that whereas UEV-1 can interact with C. elegans UBC-13, global levels of K63-linked ubiquitination throughout nematodes appear to be unaffected in uev-1 mutants, even though UEV-1 is broadly expressed in most tissues. Nevertheless, ubc-13 mutants are similar in phenotype to uev-1 mutants, suggesting that the two proteins do work together to regulate GLR-1 trafficking. Our results suggest that UEV-1 could regulate a small subset of K63-linked ubiquitination events in nematodes, at least one of which is critical in regulating GLR-1 trafficking.

Figure 1. UEV-1 regulates GLR-1 Trafficking.

The fluorescence of (A, B) GLR-1::GFP (GluR), (C, D) SNB-1::GFP (synaptobrevin), (E, F) LIN-10::GFP (Mint2), and (G, H) UNC-43::GFP (CaMKII) was observed along ventral cord neurites of (A, C, E, G) wild-type or (B, D, F, H) uev-1(od10)-mutant animals. The mean size (I) of fluorescent puncta and accretions (arrows) combined are plotted for adult nematodes of the given genotype (stippled bars for wild type, gray bars for uev-1 mutants) and for the given fluorescent reporter (indicated below the graph). (J) The mean density (number per 10 microns of ventral cord length) of fluorescent puncta is plotted for adults of the given genotype. For each genotype, the values have been normalized to the mean value of the wild-type control. Whereas wild-type animals have small GLR-1::GFP puncta, uev-1 mutants accumulate GLR-1::GFP in large accretions (arrows); other synaptic proteins appear not to be affected in uev-1 mutants. Bar, 5 microns. Error bars are SEM. N = 20–30 animals for each genotype. *P<0.01, ***P<0.001 by ANOVA with Bonferroni multiple comparison tests (only shown for wild type versus mutant for each reporter).

Figure 2. UEV-1 is a member of the E2 ubiquitin-conjugating enzyme variant family.

(A) The intron/exon structure of uev-1 based on sequenced cDNAs is shown in the top panel. Gray boxes indicate exonic coding sequences. The arrow indicates the start of transcription. The site of the od10 molecular lesion is indicated. Predicted alpha helices and beta sheets, based on alignment with human MMS2, are indicated . The purple line indicates the sequences that are removed by the ok2610 deletion. The bottom panel shows the amino acid alignment of C. elegans (C.e.) uev-1 with its two putative homologs in humans (H.s.), UBE2V1/UEV1 and UBE2V2/MMS2, along with Mms2 from yeast (S.c.). Black highlighting indicates identity, and gray indicates similarity. The locations of the F8 residue (mutated in our binding constructs) and the residue altered in od10 to nonsense are indicated. Predicted alpha helices and beta sheets are indicated below the aligned sequence. (B–E) GLR-1::GFP fluorescence in the ventral cord from (B) wild type, (C) uev-1(od10) homozygotes, (D) uev-1(od10) containing the P_glr-1::uev-1(+) transgene, and (E) uev-1(ok2610) homozygotes. The mean number of (F) GLR-1::GFP puncta and (G) GLR-1::GFP accretions per 100 micron of ventral cord length is indicated for the given genotypes. Cell autonomous expression of wild-type uev-1 via the glr-1 promoter is sufficient to rescue uev-1 mutants. Bar, 5 microns. Error bars are SEM. N = 20–30 animals for each genotype. **P<0.01 by ANOVA with Dunnett's multiple comparison to wild type.

Figure 3. UEV-1 is broadly expressed.

(A–F) Fluorescence from animals transgenic for P_uev-1::uev-1::gfp. Expression is detected in (A) pharynx and multiple head neurons, (B) distal tip cell, vulval epithelia, and ventral cord motoneurons (arrowheads), (C) most cells of embryos (gastrulating embryo shown from ventral view), (D) intestinal epithelia and motoneurons (arrowheads), (E) body wall muscle, and (F) ventral cord motoneurons. (D–F) Arrows indicate nuclear enrichment of the UEV-1::GFP protein. (G–L) Fluorescence from uev-1(od10)-mutant animals co-expressing (G, J) GLR-1::GFP and (H, K) mCherry::UEV-1 via the glr-1 promoter. (I, L) Merged images. (G–I) UEV-1 is enriched in nuclei (arrow), but can be found at punctate structures in the cell body cytoplasm (PVC neuron cell body is shown). (J–L) UEV-1 is uniformly distributed along ventral cord neurites. Bar, 5 microns.

Figure 4. UEV-1 is required for motoneuron synaptic bouton differentiation.

(A–D) Fluorescence from animals transgenic for P_unc-25::snb-1::gfp (synaptobrevin). (A) Presynaptic boutons labeled with SNB-1::GFP are distinct along the dorsal and ventral cords of wild-type animals. Such boutons are missing, irregular in shape and size, and/or abnormally spaced in (C) uev-1(od10) mutants, a phenotype reminiscent of that observed in (B) rpm-1 mutants. (D) Mutations in pmk-3 do not alter the uev-1 phenotype. (E) The total number of dorsal cord SNB-1::GFP puncta is plotted for the indicated genotypes. (F) GLR-1::GFP accumulation in accretions in uev-1 pmk-3 double mutants is similar to that observed in uev-1(od10) single mutants. Bar, 5 microns. Error bars are SEM. N = 20–30 animals for each genotype. ***P<0.001 by ANOVA with Bonferroni multiple comparison tests.

Figure 5. UEV-1 regulates both GLR-1 levels and spatial distribution.

(A–H) GLR-1::GFP fluorescence in (A, C, E, G) neuron cell bodies and (B, D, F, H) along the ventral cord for (A, B) wild type, (C, D) uev-1(od10) mutants, (E, F) ire-1 mutants, and (G, H) ire-1 uev-1 double mutants. To quantify the unusual spatial distribution of GLR-1 in uev-1 mutants, the region 65 microns anterior (left in the figure) of the RIG/AVG cell bodies (these neurons contribute little GLR-1::GFP to the ventral cord, used here solely as a landmark) was considered as “proximal” to the neuron cell bodies of the command neurons in the head (AVA, AVB, AVD, AVE, and PVC, which contribute almost all of the GLR-1::GFP along the ventral and are outside of the images in this figure), whereas the region 65 microns posterior (right in the figure) of the RIG/AVG cell bodies were considered as “distal” to the command neuron cell bodies. The images in E–H were collected at several times the exposure as the images in A–D as no single exposure time possessed the dynamic range to precisely capture all four genotypes. (I) Line profiles for GLR-1::GFP fluorescent intensity along the ventral cord for a wild-type animal (blue) and a uev-1(od10) mutant (red) after removal of background autofluorescence. Baseline is a measure of unlocalized GLR-1::GFP levels. Brighter GLR-1::GFP puncta are observed more proximal along the neurites to the cell bodies. This proximal-distal bias is increased in uev-1 mutants compared to wild type. (J) Mean GLR-1::GFP fluorescence (sum of pixel values) along the ventral cord for either the total cord, the proximal region, or the distal region for wild type (stippled) or uev-1 mutants (gray). (K, L) GLR-1::GFP fluorescence (sum of pixel values) observed in the PVC neuron cell bodies for the indicated genotypes. (M) Mean number of GLR-1::GFP puncta along the ventral cord (per 100 micron length) for either the total cord, the proximal region, or the distal region for wild type (stippled) or uev-1(od10) mutants (gray). Bar, 5 microns. Error bars are SEM. N = 20–30 animals for each genotype. (J, M) **P<0.01, ***P<0.001 by ANOVA with Bonferroni multiple comparison tests (only shown for wild type versus mutant for each reporter). (K, L) *P<0.01, ***P<0.0001 by t-test.

Figure 6. UEV-1 regulates GLR-1 colocalization with endosomal protein RAB-10.

(A, E) GLR-1::GFP and (B, F) mRFP::RAB-10 fluorescence was observed in single-plane confocal images of PVC neuron cell bodies from (A–D) wild-type animals and (E–H) uev-1(od10) mutants. (C, G) Merged images. (D, H) Binary masks (yellow) were created to highlight pixels with matching intensity values for both GLR-1::GFP and mRFP::RAB-10, indicating colocalization. The mean percent of (I) GLR-1 colocalized with RAB-10, and (J) RAB-10 colocalized with GLR-1 is plotted for the indicated genotypes. More GLR-1 is found colocalized with RAB-10 in uev-1(od10) mutants. (K) The mean spontaneous reversal frequency as an indication of GLR-1 function is plotted for the indicated genotypes. The mean percent of (L) GLR-1::GFP colocalized with Syntaxin-13::mRFP, and (M) Syntaxin-13::mRFP colocalized with GLR-1::GFP is plotted for the indicated genotypes. Bar, 1 microns. Error bars are SEM. N = 20–30 animals for each genotype. (I, J) ***P<0.0001, *P<0.05 by t-test. (K) **P<0.01, *P<0.05 by ANOVA with Dunnett's multiple comparison test to wild type.

Figure 7. UEV-1-dependent trafficking of GLR-1 is independent of clathrin-mediated endocytosis.

(A-H) GLR-1::GFP ventral cord fluorescence is shown for the indicated genotypes: (A) wild type, (B) uev-1, (C) itsn-1, (D) itsn-1 uev-1, (E) lin-10, (F) lin-10 uev-1, (G) rab-10, and (H) rab-10 uev-1. The uev-1(ok2610) allele was used in these experiments. Mean (I, K) size and (J, L) number of GLR-1::GFP accretions observed along the ventral cord of the indicated genotypes. Bar, 5 microns. Error bars are SEM. N = 20–30 animals for each genotype. ***P<0.001, **P<0.01, *P<0.05 by ANOVA with Bonferroni multiple comparison tests. For (K) and (L), only comparisons between double mutants and their corresponding single mutants are shown for clarity.

Figure 8. UEV-1 and ubiquitin-mediated turnover of GLR-1.

(A–D) GLR-1::GFP ventral cord fluorescence in (A) wild type, (B) uev-1(od10) mutants, (C) wild type that overexpress free ubiquitin, and (D) uev-1(od10) mutants that overexpress free ubiquitin. (E, F) GLR-1(4KR)::GFP ventral cord fluorescence in (E) wild type and (F) uev-1(od10) mutants. The mean (G, I) number and (H, J) size of GLR-1::GFP accretions is plotted for the indicated genotypes. In (I–J), “GLR-1(+)” indicates the presence of the wild-type GLR-1::GFP-expressing transgene, whereas “GLR-1(4KR)” indicates the presence of the GLR-1(4KR)::GFP-expressing transgene; GLR-1(4KR)::GFP cannot be ubiquitinated. Bar, 5 microns. Error bars are SEM. N = 20–30 animals for each genotype. ***P<0.001 by ANOVA with Bonferroni multiple comparison tests.

Figure 9. UEV-1 interacts with UBC-13 to regulate GLR-1.

(A) Top left panel shows a Coomasie-stained SDS-PAGE for bacterially produced GST and GST::UBC-13 used in the pull down assay. Top right panel shows a Western blot using anti-GFP antibodies to detect GFP::UEV-1 or GFP::UEV-1(F8A) pulled down from COS7 lysates using either GST or GST::UBC-13 bound to beads. “Input” indicates 10% of the lysate used in the binding reaction. Arrow indicates the specific GFP::UEV-1 protein. Arrowheads indicate non-specific bands in the lysate that are pulled down by GST::UBC-13 and detected on the Western blot. Bottom panel shows growth on media either selecting for interaction (–Leu –His –Trp) or allowing growth without selection (–His –Trp) for 10 fold serial dilutions of yeast cultures co-expressing the indicated bait and prey plasmids. Similar results were found in 3 independent experiments. (B) Western blots for K63-linked polyubiquitinated proteins or actin as a loading control. Purified tetra-ubiquitin (Ub4) is present on the SDS-PAGE in either the K63-linked form (which runs at around 25 kDa) or the K48-linked form (which runs at around 30 kDa). Coomasie-stained SDS-PAGE for each tetra-ubiquitin protein is also shown. Similar results were found in 5 independent experiments. (C) GLR-1::GFP fluorescence from either cell bodies (left hand panels) or neurites around the retrovesicular region (right hand panels) are shown for the indicated genotypes. Like uev-1 mutants, ubc-13(tm3546) mutants accumulate GLR-1::GFP in their cell bodies and at proximal regions along their ventral cord neurites. Bar, 5 microns. The (D) number of GLR-1::GFP puncta, (E) number of GLR-1::GFP accretions, and (F) size of GLR-1::GFP accretions are indicated for the given genotypes. *P<0.05, **P<0.01, ***P<0.001 by ANOVA with Dunnett's comparison to wild type. Error bars are SEM. N = 20–30 animals for each genotype.

Figure 10. A model for UEV-1 function.

Previous results indicate that GLR-1 is endocytosed and recycled by two pathways: a clathrin-dependent pathway (which involves ITSN-1 and RAB-5) that requires LIN-10 for recycling, and a clathrin-independent pathway that requires RAB-10 for recycling. Based on genetic and cell biological data, we suggest that UEV-1 functions in the clathrin independent pathway to move receptors out of endosomes for recycling and for turnover. (A) Cartoon illustrating both pathways at different synapses along the ventral cord of wild-type animals. GLR-1 receptors (red) are being endocytosed and recycled by either the clathrin-independent endocytosis pathway (CIE) and RAB-10 (the synapse on the left) or the clathrin-dependent endocytosis pathway (CDE) and LIN-10 (the synapse on the right). Our results suggest that the more proximal synapses favor the clathrin-independent, UEV-1 dependent pathway. (B) Cartoon illustrating that the clathrin-independent pathway is disrupted in uev-1 mutants, resulting in the internalization of GLR-1 receptors into accretions due to their failure to exit endosomal compartments.