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Recipient of an RPB Senior Investigator award and an RPB Nelson Trust award. To whom correspondence may be addressed: Dept. of Ophthalmology and Visual Sciences, University of Utah Health Science Center, 65 Mario Capecchi Dr., Salt Lake City, UT 84132. Tel.:801-585-6643
Department of Ophthalmology and Visual Sciences, University of Utah Health Science Center, Salt Lake City, Utah 84132Departments of Neurobiology and AnatomyBiology, University of Utah, Salt Lake City, Utah 84112
RAB28, a member of the RAS oncogene family, is a ubiquitous, farnesylated, small GTPase of unknown function present in photoreceptors and the retinal pigmented epithelium (RPE). Nonsense mutations of the human RAB28 gene cause recessive cone-rod dystrophy 18 (CRD18), characterized by macular hyperpigmentation, progressive loss of visual acuity, RPE atrophy, and severely attenuated cone and rod electroretinography (ERG) responses. In an attempt to elucidate the disease-causing mechanism, we generated Rab28−/− mice by deleting exon 3 and truncating RAB28 after exon 2. We found that Rab28−/− mice recapitulate features of the human dystrophy (i.e. they exhibited reduced cone and rod ERG responses and progressive retina degeneration). Cones of Rab28−/− mice extended their outer segments (OSs) to the RPE apical processes and formed enlarged, balloon-like distal tips before undergoing degeneration. The visual pigment content of WT and Rab28−/− cones was comparable before the onset of degeneration. Cone phagosomes were almost absent in Rab28−/− mice, whereas rod phagosomes displayed normal levels. A protein–protein interaction screen identified several RAB28-interacting proteins, including the prenyl-binding protein phosphodiesterase 6 δ-subunit (PDE6D) and voltage-gated potassium channel subfamily J member 13 (KCNJ13) present in the RPE apical processes. Of note, the loss of PDE6D prevented delivery of RAB28 to OSs. Taken together, these findings reveal that RAB28 is required for shedding and phagocytosis of cone OS discs.
Mammalian photoreceptors renew one-tenth of the OS
Whereas the molecular basis underlying CRD18 has been obscure, our study suggests that RAB28 is an essential factor in cone-specific disc shedding and phagocytosis. In Rab28 germ line knockout mice, which recapitulate the human CRD18 phenotype, we found that mutant cones elongate and form enlarged tips as early as P14, suggesting a disc shedding impairment. RAB28 traffics to the photoreceptor OS in a complex with PDE6D. Further, RAB28 interacts with KCNJ13, a potassium channel in the RPE associated with Leber congenital amaurosis (LCA16); KCNJ13 may collaborate with RAB28 to facilitate COS phagocytosis.
The murine Rab28 gene and splice variants
The mouse Rab28 gene consists of nine exons and expresses three splice variants, V1–V3. The variants share amino acids 1–191 encoded by exons 1–6 but differ in their C-terminals, encoded by exons 8, 7, and 9, respectively (Fig. 1A). RAB28V1 (221 amino acids) and V2 (220 amino acids) carry a CAAX box sequence, where X = Q predicts farnesylation. RAB28V3 (191 amino acids) has a shorter C-terminal region and is not prenylated. The polyclonal RAB28 antibody used in this study recognized both V1 and V2 recombinant proteins (Fig. 1B) and thus should also recognize V3. Recombinant variants V1 and V2 are present in the HEK293 cell body, and V2 appears to be translocated selectively into the nucleus (Fig. 1C).
Generation of Rab28 gene trap (GT) and knockout mice
Rab28GT/GT mutant mice carrying a GT cassette in intron 2 and a floxed exon 3 were generated using a EUCOMM cell line. Correct gene targeting was verified by sequencing of PCR-amplified 3′ and 5′ recombination arms and FRT and LoxP sites (Fig. 1, D and E). To avoid interference of the GT cassette on nearby gene expression, we generated a Rab28 floxed allele (Rab28fl/+) by crossing Rab28GT/GT with flippase mice; the knockout allele (Rab28+/−) was generated subsequently by mating Rab28fl/+ with CMV-Cre mice. Rab28−/− mice are viable and fertile. RAB28 protein variants of 25-kDa mobility are undetectable in Rab28−/− retina lysates by immunoblotting (Fig. 1F); variant V3 is not expressed at detectable levels in WT samples. In WT retina cryosections, RAB28 is expressed in the RPE and all photoreceptor compartments, most strongly in outer segments (Fig. 1G, left); no variant is detectable in Rab28−/− retina cryosections (Fig. 1G, right). When electroporated into Rab28−/− rods, mCherry-RAB28V2 distributes throughout the cell (Fig. 1H).
Rab28−/− mice recapitulate human CRD18
Photoreceptor function was evaluated by scotopic and photopic ERG testing over a period of 13 months. At 3 months of age, both scotopic (rod) and photopic (cone) responses are significantly reduced in Rab28−/− mice, with greater reduction in photopic b-wave amplitudes. Mutant scotopic a-wave amplitudes are reduced to ∼70% of control (Fig. 2, A and C), whereas the photopic b-wave amplitude is <50% (Fig. 2, B and D). Retina dystrophy of human CRD18 patients is typically diagnosed in early childhood (
Immunolabeling of Rab28−/− retina with antibodies directed against guanylate cyclase 1 (GC1) or mouse cone arrestin revealed fast degeneration of cones, accompanied by progressive ROS shortening and a mild reduction of ONL thickness (Fig. 3A). The cone number is slightly reduced (88% of control) at 1 month (Fig. 3, A and F), but severely reduced at 3 months, and very few cones are detectable at 13 months (Fig. 3A, bottom panels). Accordingly, the scotopic a-wave amplitude declines slowly starting at 1 month, and by 13 months, it is 42% of WT controls (Fig. 3B). Photopic ERGs decline much faster and are attenuated at all tested time points, at 65% of control at 1 month and undetectable at 13 months (Fig. 3C). ONL thickness in the central retina is reduced to 87, 78, and 73% of controls by 3, 6, and 13 months of age (Fig. 3D), respectively, whereas mutant retina OS lengths are reduced to 69, 65, and 50% at 3, 6, and 13 months (Fig. 3E). Cone densities are reduced to 88, 71, 35, and 12% of control levels at 1, 3, 6, and 13 months, respectively (Fig. 3F).
Rab28−/− cones have elongated OS and enlarged OS tips
All examined rod proteins (rhodopsin, transducin, PDE6, and CNGA1) were correctly localized to the ROS of 1-month-old mutants (Fig. 4A, bottom panels). By contrast, visual pigments ML-opsin and S-opsin mislocalized in part to the IS, ONL, and OPL of mutant cones (Fig. 4 (C and D), red arrows). We further observed that mutant COS are elongated, stretching toward the apical RPE edge, and frequently display a bulge at the distal tip revealed by CNGA3 and cone opsin immunolabeling (Fig. 4 (B–D), white arrows). Whereas WT COS taper toward their tips (Fig. 4F), mutant COS exhibit enlarged, balloon-like tips carried by elongated and slender outer segments (Fig. 4, G and H). One-month-old mutant COS (21.7 ± 4.9 μm) average 43% longer than control COS (15.1 ± 1.6 μm) (Fig. 4I). Slight elongation of mutant COS and occasional COS tip enlargement are first observed shortly after eye opening (P12), which suggests a defect in COS membrane shedding and RPE phagocytosis (Fig. 4E).
A second observation gleaned from immunohistochemistry was that levels of prenylated OS proteins (G protein–coupled receptor kinase 1 (GRK1), cone PDE α-subunit (cPDEα′), and cone transducin γ-subunit (cTγ)) appear reduced in mutant cones (Fig. 5 (A–C), bottom panels). Reduction of GRK1 levels in mutant cones could be observed as early as P14 (Fig. 5D), whereas GRK1 levels in ROS appear comparable at both P14 and 1 month of age (Fig. 5, A and D). Western blotting using 7-week-old retina lysates showed that Rab28−/− COS protein levels, including cPDEα′ and GRK1, are comparable with heterozygous controls (Fig. 5, E and F). The reduction of cTγ and cPDEγ was statistically significant (Fig. 5F). Western blotting with 3-week-old retina lysates did not display significant differences in COS protein levels (results not shown).
Phagocytosis defects of Rab28−/− cones
To evaluate COS membrane shedding defects, we harvested P24 WT and mutant retinas 1.5 h after light onset and labeled fixed cryosections with combined ML- and S-opsin antibodies. At this time, cone opsin–positive phagosomes (green) are located within the apical RPE microvilli or RPE somata (Fig. 6A, white arrows; cone sheaths identified using peanut agglutinin (PNA; red)). The number of COS phagosomes is reduced in mutant retina where the COS tip enlargement is already obvious (Fig. 6B, arrows). Rab28−/− COS phagosome counts (Fig. 6C) revealed a 5-fold reduction (7.5 ± 2.6 per 2-mm retina) compared with WT controls (39.8 ± 6.0 per 2-mm retina). In contrast, the rod phagosome density is comparable in P24 WT and Rab28−/− retinas (Fig. 6, D and E), by statistical evaluation, amounting to 56.3 ± 7.1 per 200-μm control RPE versus 51.4 ± 3.5 per 200-μm Rab28−/− RPE (Fig. 6F). These results are interpreted to indicate that Rab28−/− COS membrane shedding is defective, whereas ROS phagocytosis proceeds normally.
The Nrl−/− mouse expresses “S-cone–like” photoreceptors and is a model for enhanced S-cone syndrome in which cone phagocytosis is impaired (
). We generated Rab28−/−; Nrl−/− double knockouts to analyze COS phagocytosis. We observed that Rab28−/−; Nrl−/− cone tips were larger than in Nrl−/− controls (Fig. 6G, arrows) and that cone phagosomes could not be recorded in single (Fig. 6G) or double knockout mutants (Fig. 6H), consistent with another study (
). Larger tips in Rab28−/−; Nrl−/− cones suggest a more dramatic accumulation of unshed membrane relative to Nrl−/− S-cones.
Accumulation of material in Rab28−/− COS tip
Transmission EM of 1-month-old Rab28−/− and heterozygous control retinas documented elongated cones with disorganized distal membranes in mutants (Fig. 7, A and B). At the Rab28−/− RPE/photoreceptor interface, we observed RPE microvilli-wrapped structures filled with distorted membrane stacks or vacuolar membranes (Fig. 7, C and D). These structures appear in different shapes (round and oblique) at least 2 μm in size (Fig. 7, F and G), indicating buildup of materials at the OS tip. The size of the vacuoles (Fig. 7 (F and G), yellow arrows) and the shapes of membrane stacks (Fig. 7 (F and G), arrowheads) within these bulbous structures also vary. As these structures correspond to the bulges of COS tips seen in Rab28−/− immunostaining (Fig. 4), the variable-size vacuoles and distorted membranes stacks may represent different stages of COS degeneration. Additionally, there are increased RPE pigment deposits in Rab28−/− compared with Rab28+/− controls (Fig. 7 (C and D), dashed arrows). By contrast, ROS disc morphology appears to be normal in Rab28−/− rods (Fig. 7H).
RAB28 interacts with KCNJ13, an RPE microvillus protein
Co-immunoprecipitation (co-IP) using bovine retina lysates followed by MS was performed to identify interacting proteins. We identified dozens of potential interactors (t test, p < 0.05, RAB28 IP/control IP ratio >3, Table S2). Top candidates include the prenyl-binding protein PDE6D, which has been reported previously to interact with RAB28 (
). In selective Western blotting verification, we successfully verified the interaction of RAB28 with KCNJ13, MEF2D, GLUT1, VAC14, and PDE6D, but failed to validate GRK1 and CAND1 (Fig. 8A), indicating high reliability of our co-IP results.
KCNJ13 is located at the root of WT apical RPE microvilli (
) and overlaps with the cone sheath marker, PNA (Fig. 8B). This pattern is preserved in Rab28−/− (Fig. 8C). Because the possible alteration of KCNJ13 localization on cone-associated microvilli could be masked by the overwhelming signal of rod-associated microvilli, we determined the KCNJ13 localization in Rab28−/−; Nrl−/− mice. KCNJ13 is located at the RPE microvilli that span the entire short OS in Nrl−/− control animals (Fig. 8D). However, in Rab28−/−; Nrl−/− double knockout mice, KCNJ13 is partially trapped at the base of apical RPE microvilli (Fig. 8E), suggesting a role of RAB28 in KCNJ13 microvilli trafficking.
RAB28 is PDE cargo targeted for the OS
To elucidate the nature of PDE6D–RAB28 interaction, we co-expressed PDE6D-EGFP and mCherry-RAB28V2 in HEK293 cells and repeated co-immunoprecipitation using mCherry antibody. As expected, mCherry-RAB28V2 co-precipitated PDE6D-EGFP (Fig. 9A). However, mCherry-RAB28V2-C217A, in which the cysteine of the CAAX box motif is mutated to alanine, preventing farnesylation, is unable to interact with PDE6D-EGFP, indicating that the interaction is RAB28 prenylation-dependent (Fig. 9A). Nonfarnesylated mCherry-Rab29V2-C217A distributed evenly within the cell due to the loss of membrane association (Fig. 9B). In PDE6d−/− mice, RAB28 is absent in the OS but accumulates in the IS (Fig. 9C), verifying that RAB28 is a PDE6D cargo, as observed for other prenylated OS proteins (
In this study, we show that Rab28 germ line knockout mice recapitulate the human CRD18 phenotype. In human CRD patients, the RAB28 gene carries nonsense mutations in exons 5 and 6, truncating all known splice variants (
). CRD may be accompanied by visual acuity deterioration, absence of photopic ERG responses, and myopia as early as age 16. In the Rab28−/− mouse model, photopic b-waves are reduced at 1 month and nearly absent by 1 year of age, which is roughly consistent with human CRD (Figure 2, Figure 3).
We found that Rab28−/− COS are elongated to the length of rod outer segments, and the mutant tips are expanded to balloon-like structures and appear unable to shed membranes to be phagocytosed by the RPE. In view of impaired disc shedding at the distal cone outer segment, continued overproduction of new disc membranes at the proximal end may provide a jammed gate impenetrable for prenylated proteins (see the model in Fig. 10). The absence of membrane shedding is supported by dramatic reduction of cone pigment–containing phagosomes (Fig. 6). Bulbous OS tips and lack of phagosome production was also observed in the Nrl−/− mouse, a model for enhanced S-cone syndrome (
). Rab28−/− COS elongation and enlarged COS tips were observed shortly after eye opening (Fig. 4). We propose that CRD18 is caused by impaired membrane shedding at the distal COS and/or failed phagocytosis by the RPE. The resulting accumulation is detrimental for cone survival. The molecular identities of components involved in human and mouse disc shedding are currently unclear. Human cone membrane shedding, observed in vivo by adaptive optics optical coherence tomography (
), was characterized by abrupt and transient loss of the COS tip. Average duration of tip loss was ∼9 min, and average length loss was reported as 2.1 μm.
In 1-month-old Rab28−/− retina, COS are elongated, and COS distal tips are filled with vacuoles and/or distorted membranes (Fig. 7). The accumulated membranes resemble material observed in degenerating Nrl−/− mouse cones at 8 weeks of age (
), indicating that Rab28−/− COS degeneration starts earlier and is more severe. Another notable observation is that both Rab28−/− and Nrl−/− showed COS disorganization at the disc periphery. The Rab28−/− disc edge shows merger/swelling or disassembly (Fig. 7B), whereas the Nrl−/− disc edge reveals interconnection (
), suggesting that the COS disc edge is vulnerable to the accumulation of oxidative materials.
Bulbous Rab28−/− OS tips are only observed in mutant cones, as mutant rods are initially unaffected and shed discs exhibit a normal phagosome count (Fig. 6). The reason for this specificity is unknown. ROS phagocytosis is triggered by diurnal surface exposure of the anionic phospholipid phosphatidylserine at the OS tip (
), their participation in COS recognition and binding is unlikely. A recent large-cohort genetic study of inherited retina diseases found that MerTK mutations exist in a small percentage of CRD patients (
), the failed Rab28−/− shedding phenotype may indicate a communication defect between RPE microvilli and mutant COS tips.
Our protein–protein interaction screen identified the RPE microvilli–resident protein, KCNJ13, as a RAB28 interactant. Recessive mutations of KCNJ13 are associated with LCA16 in humans, with an undefined mechanism (
). We found that KCNJ13 delivery to RPE microvilli in Rab28−/−; Nrl−/− double knockout is partially reduced (Fig. 8), providing a clue that RPE phagocytosis may be impaired as well. We speculate that absence of RAB28 may alter the KCNJ13 activity, which in turn affects the function of RPE microvilli and cone phagocytosis.
A second important RAB28 interactant is PDE6D, a prenyl-binding protein. A Pde6d−/− mouse develops recessive CRD in which prenylated OS proteins (cPDEα′, GRK1) are absent in the COS (
). Our finding that farnesylated RAB28 is unable to traffic to the OS in the absence of PDE6D (Fig. 9C) raises the interesting point that the cone-rod dystrophy in PDE6d mutant mice may result partly from the absence of RAB28 in cones. A PDE6D null allele in human patients was associated with Joubert syndrome and shown to impair trafficking of INPP5E, a phosphatidylinositol polyphosphate phosphatase involved in phosphatidylinositol metabolism (
The Rab28−/− mouse model provides evidence that CRD18 is caused by a defect in cone disc shedding. Owing to continuous renewal of membranes containing phototransduction components at the proximal OS and the absence of disc shedding, mutant OSs stretch toward the RPE and expand their tips to a balloon-like structure. Cone pigment–containing phagosomes are dramatically reduced. However, because RPE and cones collaborate in phagocytosis and RAB28 is normally expressed in the RPE, a role of the Rab28−/− in defective RPE phagocytosis cannot be excluded.
Animal procedures were approved by the University of Utah institutional animal care and use committee and were conducted in compliance with the National Institutes of Health Guide for Care and Use of Laboratory Animals.
Generation of Rab28−/− mouse
Rab28 embryonic stem (ES) cells (clones EPD0688_3_D01 and HEPD0677_7_A05), in C57BL/6N genetic background, JM8A3.N1 subline) containing a gene trap in intron 2 were acquired from EUCOMM (Helmholtz Zentrum, Munich, Germany). ES cell blastocyst injection, generation of chimera, and generation/breeding of heterozygous (GT/+) mice were performed at the University of Utah transgenic core. The rd8 mutation (
) was removed by crossing our Rab28GT/+ animals with C57BL/J WT mice. We crossed Rab28GT/GT with flippase mice (C57BL/6 background) to generate animals with a floxed allele (Rab28fl/+) (Fig. 1D). Exon 3 was deleted by crossing Rab28fl/fl with CMV-Cre mice (C57BL/6 background) to generate Rab28+/− and Rab28−/− mice. Mice were maintained under 12-h cyclic dark/light conditions. ES cell and mouse tail genomic DNA was extracted using a standard protocol (
). PCR genotyping primers and other primers (see below) are listed in Table S1.
RNA extraction, RT-PCR, and plasmid construction
Retina tissues were dissected from WT mice, and total RNA was extracted using TRIzol reagent (Invitrogen). Reverse transcription was performed using SuperScript II reverse transcriptase (with random primers) following the manufacturer's instructions. Full-length RAB28V1 and RAB28V2 were amplified by PCR and cloned into pEGFP-C1 and pmCherry-C1 (Clontech), respectively. PDE6D-EGFP was kindly provided by Dr. Houbin Zhang (University of Electronic Science and Technology of China, Chengdu). Nonprenylated RAB28V2-C217A was generated using the Phusion site-directed mutagenesis kit (Thermo Fisher Scientific). All plasmids were verified by Sanger sequencing.
ERG was performed on 1-, 3-, 6-, and 13-month-old Rab28−/− and WT control animals (n = 5 each group) using an UTAS E-3000 universal electrophysiological system (LKC Technologies) as described (
). Briefly, mice were dark-adapted overnight, anesthetized by intraperitoneal injection of ketamine (100 μg/g body weight) and xylazine (10 μg/g body weight) in 0.1 m PBS, and loaded onto a recording platform with body temperature maintained at 37 ± 0.5 °C. After dilating pupils with 1% tropicamide solution (Bausch & Lomb Inc., Tampa, FL), ERG responses were recorded from five mice of each genotype per time point. For scotopic ERG, mice were tested at intensities ranging from −1.63 to 2.38 log cd s/m2. For photopic ERG, a rod saturating background light of 1.3979 log cd s/m2 was applied for 20 min before and during recording at −0.01 to 1.86 log cd s/m2. Bactitracin ophthalmic ointment (Perrigo, Minneapolis, MN) was routinely applied to the eye to prevent infection after ERG testing, and animals were kept on heating pads until fully recovered before being returned to cages. Peak amplitudes for both a- and b-waves were used for analysis using a one-way ANOVA test.
Measurement of ONL thickness and OS length
Average ONL thickness and OS length were measured based on DAPI and anti-GC1 antibody fluorescence (
) with minor modifications. Eyecups were fixed by immersion in ice-cold 4% paraformaldehyde, cryoprotected in 30% sucrose, and embedded in OCT compound. Sections (12 μm thick) were cut using a Micron cryostat and mounted on charged Superfrost® Plus slides (Fisher). Sections were washed in 0.1 m PBS, blocked using 10% normal goat serum or 2% BSA, 0.3% Triton X-100 in PBS, and incubated with primary antibodies at 4 °C overnight. After washes in PBS, signals were detected with Cy3-conjugated or Alexa 488–conjugated goat anti-rabbit/mouse and/or donkey anti-goat/rabbit/mouse secondary antibody (Jackson ImmunoResearch, Inc.) and counterstained with 1 μl/ml DAPI (Invitrogen). Primary antibodies were as follows: goat anti-RAB28 (Biorbyt), mouse monoclonal anti-rhodopsin (1D4; 1:1000), anti-ROM-1 (1:25) (Dr. Robert Molday, University of British Columbia), anti-GC1 (IS4; 1:1000; Dr. Kris Palczewski, Case Western Reserve University), cyclic nucleotide–gated channel α 1 and 3 (CNGA1/A3) (1:1000; NeuroMab, University of California, Davis, CA), GRK1 (G8, Santa Cruz Biotechnology, Inc.; 1:300); rabbit polyclonal anti-ML- and S-opsin (Chemicon; 1:1500), CNGA3 (1:500; Dr. Xi-Qin Ding, University of Oklahoma), cTγ (Cytosignal; 1:500), cone arrestin (mCAR; 1:500) (
), PDE6 (MOE, Cytosignal; 1:1500), rod transducin α (Cytosignal; 1:500), and cone PDE6α′ (Dr. Tiansen Li, NEI, National Institutes of Health; 1:40,000). Images were captured using a Zeiss LSM-800 confocal microscope. Some images were adjusted for brightness and contrast using Adobe Photoshop CS3.
Retina protein extraction and Western blotting
Retinas from WT and Rab28−/− mice or bovine were homogenized in radioimmune precipitation assay buffer (10 mm Tris-Cl, pH 8.0, 140 mm NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1 mm EDTA, 1 mm phenylmethylsulfonyl fluoride) and centrifuged (13,000 × g, 4 °C, for 20 min), and supernatants were collected. Protein samples were separated by 10–12% SDS-PAGE, transferred to polyvinylidene difluoride membrane, and probed with primary antibodies followed by horseradish peroxidase–conjugated secondary antibody. Antigens were visualized using an ECL-plus kit (Pierce).
Bovine retinas (n = 5) were pooled and homogenized in 50 ml of lysis buffer (50 mm Tris-Cl, pH 7.6, 120 mm NaCl, 0.5% IGEPAL CA-630, 1 mm phenylmethylsulfonyl fluoride, 1× protease inhibitor) using a Dounce homogenizer. Cell debris was removed by centrifugation at 3000 × g, 4 °C, for 5 min. The cleaned samples were centrifuged at 20,000 × g, 4 °C, for 30 min, and the supernatants were collected. The supernatants were precleared with 500 μl of 50% protein G–Sepharose 4 fast flow beads (GE Healthcare) for 30 min. Precleared lysates were divided into 10 aliquots (5 ml each). Half of the aliquots were each incubated with goat anti-RAB28 primary antibody (10 μg), and the other half were incubated with normal goat IgG (10 μg) for 1 h 45 min at 4 °C with gentle agitation, followed by incubation with protein G–Sepharose beads for 45 min. Beads were collected by centrifugation at 2300 × g for 1 min and washed six times in lysis buffer without protease inhibitors and once in 1× PBS. Immunoprecipitated proteins were eluted using an improved soft elution method, which minimally co-elutes immunoglobulin (
). The eluted proteins (200 μl) were incubated with 1 ml of acetone at −20 °C overnight, precipitated by centrifugation at 10,000 × g for 10 min at 4 °C, washed with 75% ethanol, and air-dried. Samples were subjected to quantitative MS.
Protein samples were subjected to in-solution tryptic cleavage, as described previously (
). LC-MS/MS analysis was performed using an Ultimate3000 nano-RSLC system (Thermo Scientific) coupled to an Orbitrap Fusion Tribrid mass spectrometer (Thermo Scientific) by a nanospray ion source. Tryptic peptide mixtures were injected automatically and loaded at a flow rate of 30 μl/min in 0.1% TFA in HPLC grade water onto a nano trap column (300-μm inner diameter × 5-mm precolumn, packed with Acclaim PepMap100 C18, 5 μm, 100 Å; Thermo Scientific). After 3 min, peptides were eluted and separated on the analytical column (75-μm inner diameter × 25 cm, Acclaim PepMap RSLC C18, 2 μm, 100 Å; Thermo Scientific) by a linear gradient from 2 to 30% of buffer B (80% actetonitrile and 0.08% formic acid in HPLC-grade water) in buffer A (2% acetonitrile and 0.1% formic acid in HPLC-grade water) at a flow rate of 300 nl/min over 85 min. Remaining peptides were eluted by a short gradient from 30 to 95% buffer B in 5 min. Analysis of the eluted peptides was performed by an LTQ Fusion mass spectrometer. From the high-resolution MS prescan at a resolution of 120,000 with a mass range of 335–1500, the most intense peptide ions were selected for fragment analysis if they were at least doubly charged. The normalized collision energy for higher-energy collisional dissociation was set to a value of 30, and the resulting fragments were detected in the ion trap. The lock mass option was activated; the background signal with a mass of 445.12003 was used as lock mass (
). As digesting enzyme, trypsin/P was selected with maximal 2 missed cleavages. Cysteine carbamidomethylation was set for fixed modifications, and oxidation of methionine and N-terminal acetylation were specified as variable modifications. The data were analyzed by label-free quantification with a minimum ratio count of 2. The first search peptide tolerance was set to 20, the main search peptide tolerance was set to 4.5 ppm, and the requantify option was selected. For peptide and protein identification, the Bos taurus subset of the Uniprot database (Release 2013_09) was used, and contaminants were detected using the MaxQuant contaminant search. A minimum peptide number of 2 and a minimum length of 7 amino acids was tolerated. Unique and razor peptides were used for quantification. The match between run options was enabled with a match time window of 0.7 min and an alignment time window of 20 min. The statistical analysis, including ratio, t test, and significance calculation, was done using the Perseus software (
HEK293 cells (ATCC) were grown in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 1× penicillin/streptomycin in a standard CO2 incubator. Cells were transfected with plasmid DNA using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. Two days following transfection, cells were fixed and imaged for protein localization, lysed in radioimmune precipitation assay buffer for Western blotting, or lysed in co-IP lysis buffer (see above) for co-IP experiments.
RAB28V2 neonatal electroporation
For retina electroporation, 0.3 μl (1.5 μg) of pmCherry-RAB28V2 plasmid DNA was electroporated into the right eye subretinal space of P0 WT mice (
1- and 2.5-month-old WT and Rab28−/− retinas were fixed 2 h in fixative (2% glutaraldehyde, 1% paraformaldehyde in 0.1 m sodium cacodylate buffer, pH 7.4) at 4 °C, post-fixed for 1 h in 1% osmium tetroxide, and stained en bloc with uranyl acetate. Washed specimens were dehydrated through an ascending series of methanol, dried in propylene oxide, and infiltrated overnight with Epon resin mix/propylene oxide (1:1) mixture, followed by 100% Epon resin for 2 days. Specimens were embedded in plastic, and the plastic was cured by incubation in a 60 °C oven for 2 days. Blocks were trimmed, and 1-μm-thick sections were cut to identify and orient photoreceptors near the optic nerve. Ultrathin sections at 60 nm were cut, placed onto slot grids with carbon-coated Formvar film (EMS, Hatfield, PA), post-stained with uranyl acetate followed by lead citrate, and finally examined using a JOEL electron microscope at 75 kV.
Data are presented as mean ± S.D., where n represents the number of mice analyzed (ERG, retina measurement, phagosome count), or experiment repeats (RAB28 co-IP). Statistical comparisons (significance level set at p < 0.05) were performed using one-way ANOVA for all experimental data.
G. Y. and W. B. conceptualization; G. Y., K. B., and J. M. F. data curation; G. Y. and J. M. F. formal analysis; G. Y., K. B., M. U., C. D. G., and J. M. F. methodology; G. Y. writing-original draft; K. B., M. U., and W. B. funding acquisition; K. B., M. U., and C. D. G. investigation; M. U. resources; W. B. project administration; W. B. writing-review and editing.
We thank the following investigators for providing antibodies directed against the named proteins: Dr. Xi-Qin Ding (University of Oklahoma) for CNGA3, Dr. Tiansen Li (NEI, National Institutes of Health) for cPDEα′, Dr. Robert Molday (University of British Columbia-Vancouver) for rhodopsin and Rom1, and Dr. Kris Palczewski (Case Western Reserve University) for GC1 IS4. Dr. Houbin Zhang (University of Electronic Science and Technology of China) provided PDE6D-EGFP plasmid.
This work was supported by National Institutes of Health Grants EY08123 and EY019298 (to W. B.) and EY014800-039003 (NEI core grant); by unrestricted grants to the University of Utah Department of Ophthalmology from Research to Prevent Blindness (New York); and by the Tistou & Charlotte Kerstan Stiftung (Tübingen, Germany). The authors declare that they have no conflicts of interest with the contents of this article. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.