Human Molecular Genetics Advance Access originally published online on March 16, 2005
Human Molecular Genetics 2005 14(9):1183-1197; doi:10.1093/hmg/ddi129
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RPGR ORF15 isoform co-localizes with RPGRIP1 at centrioles and basal bodies and interacts with nucleophosmin

1MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK, 2Department of Biochemistry, University of Leicester, Leicester LE1 7RH, UK, 3Cole Eye Institute and Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA, 4Departments of Ophthalmology and Human Genetics, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA and 5Institute for Zoology, Johannes Gutenberg-University, Mainz, Germany
* To whom correspondence should be addressed. Email: alan.wright{at}hgu.mrc.ac.uk
Received November 14, 2004; Revised February 18, 2005; Accepted March 10, 2005
| ABSTRACT |
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The ORF15 isoform of RPGR (RPGRORF15) and RPGR interacting protein 1 (RPGRIP1) are mutated in a variety of retinal dystrophies but their functions are poorly understood. Here, we show that in cultured mammalian cells both RPGRORF15 and RPGRIP1 localize to centrioles. These localizations are resistant to the microtubule destabilizing drug nocodazole and persist throughout the cell cycle. RPGR and RPGRIP1 also co-localize at basal bodies in cells with primary cilia. The C-terminal (C2) domain of RPGRORF15 (ORF15C2) is highly conserved across 13 mammalian species, suggesting that it is a functionally important domain. Using matrix-assisted laser desorption ionization time-of-flight mass spectrometry, we show that this domain interacts with a 40 kDa shuttling protein nucleophosmin (NPM). The RPGRORF15NPM interaction was confirmed by (i) yeast two-hybrid analyses; (ii) binding of both recombinant and native HeLa cell NPM to RPGRORF15 fusion proteins in vitro; (iii) co-immunoprecipitation of native NPM, RPGRORF15 and RPGRIP1 from bovine retinal extracts and of native HeLa cell NPM and transfected RPGRORF15 from cultured cells and (iv) co-localization of NPM and RPGRORF15 at metaphase centrosomes in cultured cells. NPM is a multifunctional protein chaperone that shuttles between the nucleoli and the cytoplasm and has been associated with licensing of centrosomal division. RPGR and RPGRIP1 join a growing number of centrosomal proteins involved in human disease.
| INTRODUCTION |
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The ORF15-containing isoform of the RPGR protein (RPGRORF15) is mutated in a variety of retinal dystrophies, including X-linked forms of retinitis pigmentosa (1
In the mouse retina, RPGR protein is associated with the connecting cilium of rod and cone photoreceptors, which connects the inner and outer segments (15
); this is also the case in humans and other mammalian species, but it is unclear whether it is also expressed in photoreceptor outer segments (17
,18
). An Rpgr knockout mouse shows a progressive degeneration of cone and rod photoreceptors and is associated with mislocalization of opsin-containing vesicles (15
). These vesicles are normally transported to the base of the connecting cilium by means of the minus-end directed microtubule-associated motor protein cytoplasmic dynein (19
). Here, they fuse with the plasma membrane before being transported along the ciliary plasma membrane by plus-end directed microtubule motors such as kinesin-II to the photoreceptor outer segment (20
).
The function of RPGR is unclear although structural alignment of the N-terminal half of RPGR (exons 1
11
) with RCC1, a guanine nucleotide exchange factor (GEF) for the small GTPase Ran (21
23
), suggests a role in the regulation of small GTPases. However, RPGR has not been shown to have GEF activity with Ran. Yeast two-hybrid screening of retinal libraries has shown that the RCC1-like domain (RPGRRLD) binds a novel protein of unknown function, RPGR interacting protein 1 (RPGRIP1) (24
27
). Loss-of-function mutations in RPGRIP1 cause a form of congenital retinal blindness, Leber's congenital amaurosis (28
29
) and a later onset conerod dystrophy (30
). RPGRIP1 also localizes to the connecting cilium of rod and cone photoreceptors and an Rpgrip1 knockout mouse shows progressive degeneration of rod and cone photoreceptors, with abnormal extended outer segment discs and an inability to localize RPGR to the connecting cilium (27
).
The C-terminal half of the RPGR-ORF15 isoform contains a highly repetitive glutamic acid-rich plaid domain, which is a mutation hotspot, plus a non-repetitive and basic ORF15 C-terminal domain (ORF15C2) that is reported to be conserved among human, mouse, bovine and Fugu fish (1
). The latter observation suggested that ORF15C2 may have an important functional role. Here we show that the ORF15C2 domain of RPGRORF15 interacts and co-localizes with nucleophosmin (NPM or B23). Furthermore, RPGRORF15 co-localizes with RPGRIP1 at centrioles and basal bodies of cultured mammalian cells.
| RESULTS |
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Conservation of ORF15C2
We first determined the extent of cross-species conservation of the C-terminal (C2) region of RPGRORF15 (ORF15C2), defined by a clone containing the C-terminal 83 amino acids of human RPGRORF15 (residues 10701152; GenBank accession nos AF286472 and AAC50481), which marks a relatively abrupt change in sequence composition from the acidic glutamic acid-rich plaid domain to the basic C-terminal domain (1
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Identification of NPM in protein pull-down experiments
A fusion protein containing the C-terminal 81 amino acids of bovine RPGRORF15 (bORF15C2) fused to glutathione-S-transferase (GST) was immobilized onto glutathioneSepharose beads and used to pull down ORF15C2-interacting proteins from bovine retinal and kidney extracts. Eluted proteins were separated by sodium dodecyl sulphatepolyacrylamide gel electrophoresis (SDSPAGE), and retinal extract bands that were not present in the GST vector-only control were excised, and following in-gel digestion with trypsin, peptide mass mapping was performed using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. One of the excised bands of mass 40 kDa from the retinal pull-down was identified as NPM by MALDI-TOF (Fig. 1C). The same band was prominent (but not analysed by mass spectrometry) in kidney. Other excised bands were identified as cleavage products of GST, bovine adenine nucleotide translocase, actin, ß-tubulin, eukaryotic translation elongation factor 1 gamma, pre-procollagenase and glutamate dehydrogenase. Further work was carried out on the putative interaction of ORF15C2 with NPM. The interaction of ORF15 with NPM was initially confirmed by immunoblotting using anti-NPM antibody following GSTbORF15C2 pull down from bovine retinal extracts (Fig. 1D).
Human RPGR ORF15C2 was used as bait(pAS vector) and human NPM as prey (pACT vector) to test for interaction in a yeast two-hybrid analysis. A positive interaction between NPM and hORF15C2 was shown by the ability to grow on triple selection plates lacking tryptophan (Trp), leucine (Leu) and histidine (His) (Fig. 1E). This was confirmed by testing the ability of putative interacting clones to metabolize X-gal with ß-galactosidase, as shown by formation of blue colour (data not shown).
Additional pull-down experiments were carried out using both native NPM in HeLa cell extracts and recombinant NPM. HeLa cell extracts were incubated in vitro with a purified GST human ORF15C2 fusion protein (GSThORF15C2) and GST control. After washing and elution from glutathioneSepharose beads, interacting proteins were analysed by SDSPAGE and western blots. This confirmed that native NPM from crude HeLa supernatant binds to hORF15C2 in vitro (Supplementary Material, Fig. S1A). Recombinant human NPM was also incubated with GSThORF15C2 in vitro and, after affinity purification and washing, analysis of the eluted products showed that recombinant NPM also binds hORF15C2 (Supplementary Material, Fig. S1B).
The possibility of non-specific interaction between the basic ORFC2 peptide (pI=9.64) and the acidic NPM (pI=4.64) was excluded by testing for interaction between the protein 14-3-3 (pI=4.63) and GST-tagged ORF15C2 by protein pull-down experiments. Cell extracts from the human embryonic kidney (HEK) 293 cell line, which express both 14-3-3 and NPM as native proteins, were incubated with GSTORF15C2 and GST control beads. The bound proteins were screened by western blotting using anti-14-3-3 antibody (full-length isoform) and anti-NPM. This showed no interaction between 14-3-3 and ORF15C2 but confirmed the interaction with NPM (Supplementary Material, Fig. S1C). A similar experiment with recombinant enhanced green fluorescent protein (EGFP) (pI=5.8) also failed to show interaction with ORF15C2 (data not shown), supporting the specificity of the ORF15C2NPM interaction.
Co-immunoprecipitation of NPM and RPGRORF15
To further corroborate the interaction between NPM and RPGRORF15, HeLa cells were transfected with constructs expressing EGFP fused to hORF15C2 (EGFPhORF15C2) or with an EGFP control plasmid. Anti-EGFP antibody was used to co-immunoprecipitate native NPM with EGFPhORF15C2 (Fig. 2A). A minor NPM band with slightly lower molecular weight was also identified, perhaps representing a post-translational modification or degradation product.
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In order to test whether anti-ORF15C2 antibody can co-immunoprecipitate native NPM from retina, bovine retinal rod outer segment (ROS) fractions were incubated with antibody and, after washing, the immunoprecipitated fraction was separated by SDSPAGE and western blots probed with anti-ORF15C2, anti-RPGRIP1 and anti-NPM antibodies. The results (Fig. 2B) show that RPGRORF15, RPGRIP1 and NPM are each co-immunoprecipitated from retina by anti-ORF15C2 antibody (but not by pre-immune serum or protein ASepharose beads).
NPM is predominantly present in nucleoli (31
). We therefore tried to determine whether RPGRORF15 forms part of a nuclear complex with NPM in vivo. Two different antibodies (anti-ORF15C2 and anti-ORF15CP) were used in co-immunoprecipitation experiments using bovine retinal nuclear extract (RNE). Immunoblot analysis of immunoprecipitates detected anti-NPM immunoreactive bands of the expected size,
40 kDa (Fig. 2C). NPM was not immunoprecipitated when normal rabbit IgG was used as control. However, reverse co-immunoprecipitation experiments with anti-NPM antibody did not reveal RPGRORF15 upon immunoblot analysis using ORF15 antibodies (data not shown). This is probably because of low amounts of RPGRORF15 in the NPM-containing multiprotein complex(es) in the retina. Similar sized RPGRORF15 protein bands were detected in RNE with both anti-ORF15 antibodies but the nuclear band was slightly smaller than the major bands seen in whole retinal extracts, suggesting the presence of a distinct nuclear isoform, which showed substantial (50100-fold) enrichment in nuclei (Fig. 2E). We also found a punctate pattern of nuclear labelling in cell lines using anti-RPGRORF15 antibody in cultured cells, which was absent from cells labelled with pre-immune serum (Fig. 2D).
Co-localization of RPGRORF15 and RPGRIP1 at centrosomes in cultured mammalian cells
Antibodies raised against the bovine ORF15C2 domain (anti-bORF15C2) and against a synthetic peptide (1878) from a non-repetitive region of human ORF15 (anti-hORF151878) were used in indirect immunofluorescence microscopy experiments to determine the subcellular localization of both the transfected and the native RPGRORF15 isoform in a variety of cultured cells. The expression of RPGRORF15 was first examined in cultured mammalian cells using reverse transcriptasepolymerase chain reaction (RTPCR) (Supplementary Material, Fig. S1D). This confirmed equivalent expression of RPGRORF15 transcripts across cell lines, when compared with the constitutively expressed enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPD).
COS7 cells were transfected with a vector expressing EGFPbORF15C2 fusion protein and analysed by fluorescence microscopy. Transfected cells could be identified by green fluorescence which co-localized with anti-NPM antibody in nucleoli (Fig. 3A). Constructs expressing the entire exon ORF15 were not detected in the nucleus, presumably because their size exceeds the nuclear pore diffusion limit and RPGRORF15 does not have appear to have a nuclear localization signal (NLS).
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The localization of native RPGRORF15 was examined in cultured cells expressing RPGRORF15. Two different anti-ORF15 antibodies (anti-1878 and anti-ORF15C2) co-localized with
-tubulin in U2OS and HeLa cell lines, consistent with a centrosomal localization (Fig. 3B). In certain views, it appeared that the RPGR labelling of the centrosomes formed a crescent or annular appearance (Fig. 3B, inset). Co-localization of RPGRORF15 with centrosomes was observed in all five cell lines examinedHeLa, U2OS, NIH 3T3, ARPE-19 and COS7using both anti-ORF15 antibodies. High-resolution imaging revealed two pairs of fluorescent dots in cells in G2 phase of the cell cycle, which was consistent with a specific centriolar localization (Fig. 3C). Localization of RPGRORF15 in mitotic cells revealed spindle pole labelling from prophase through to telophase (Fig. 3D).
The dependence of RPGRORF15 centrosomal localization on microtubule polymerization was examined by culturing cells in the presence and absence of the microtubule destabilizing agent nocodazole. Staining with anti-bORF15C2 and
-tubulin antibodies showed that ORF15 staining of centrosomes was resistant to treatment with nocodazole, hence it was not dependent on the presence of an intact microtubule network (Fig. 4).
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Since RPGR interacts with RPGRIP1, and the ciliary localization of RPGR is dependent on the presence of RPGRIP1, two different antibodies to RPGRIP1 were tested in the same cell lines for co-localization with RPGR by indirect immunofluorescence microscopy. The results show that both RPGRIP1 antibodies co-localized with
-tubulin in U2OS cells consistent with a centrosomal localization (Fig. 4). High resolution imaging again revealed two pairs of fluorescent dots in prophase cells consistent with centriolar localization (Fig. 4). Staining with anti-RPGRIP1 and
-tubulin antibodies showed that RPGRIP1 staining of centrosomes was again resistant to treatment with nocodazole and not dependent on microtubule polymerization (Fig. 4).
The co-localization of native RPGRORF15 and NPM was investigated in cultured mammalian cells using indirect immunofluorescence microscopy (Fig. 5). In both HeLa and U2OS cells, NPM was detected exclusively in nucleoli during interphase, but co-localized with spindle poles in mitosis. This falls in line with previous studies that NPM is a nucleolar protein (31
), but that at mitosis it can associate with spindle poles (32
). However, in contrast to this latter study (32
), we could not detect NPM at interphase centrosomes in an asynchronous population of cells. The spindle pole association of NPM precisely overlapped with the RPGRORF15 signal during metaphase but not during anaphase, when the two signals were slightly separated (Fig. 5A). During metaphase, the NPM signal extended outside of the RPGRORF15 signal, in a triangular pattern of labelling, suggesting labelling of centrosomal satellites (33
). In contrast,
-tubulin and RPGRORF15 co-localized precisely at all stages of mitosis (Fig. 5B).
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NPM immunofluorescence in the retina
In order to examine the localization of NPM in retina, bovine retinal sections were examined for NPM immunofluorescence, when compared with the centriolar and basal body protein centrin (34
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RPGR and RPGRIP1 co-localize in basal bodies
Quiescent mouse inner medullary collecting ductal epithelial (IMCD3) cells possess primary cilia growing from basal bodies which label with anti-acetylated
-tubulin antibodies. These cells were fixed and used for immunocytochemistry with anti-acetylated
-tubulin, anti-RPGRORF15 and anti-RPGRIP1 antibodies. The results show that both RPGR and RPGRIP1 co-localize at the basal bodies in IMCD3 cells (Fig. 7).
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| DISCUSSION |
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Here, we show for the first time that both RPGRORF15 and RPGRIP1 localize to centrosomes and spindle poles in cultured dividing cells. Centrosomes are complex organelles, which act as the major microtubule organizing centre for the cell (33
Both RPGRORF15 and RPGRIP1 localize to centrosomes throughout the cell cycle in all of the non-ciliated cell lines examined, including HeLa, HEK 293, COS7, NIH 3T3 and ARPE-19. Importantly, the detection of both RPGRORF15 and RPGRIP1 in four small punctate structures late in the cell cycle supports the notion that both these proteins are components of centrioles themselves rather than the surrounding pericentriolar material. RPGRIP1 may serve to anchor RPGRORF15 to the centriole in cultured cells, as it does to the ciliary axonemes of photoreceptors. Localization of both RPGRORF15 and RPGRIP1 to centrosomes is not dependent on microtubules, strengthening the hypothesis that these are core centriolar proteins and not proteins localizing to the minus-ends of cytoplasmic microtubules. In the renal medullary cell line IMCD3, which contains primary cilia nucleated by basal bodies, both RPGRORF15 and RPGRIP1 co-localize at the basal bodies. This is consistent with the close relationship between basal bodies and centrioles. Although both proteins have previously been reported to be present in photoreceptor connecting cilia, neither was known to be a component of basal bodies (18
).
Interestingly, we also show that RPGRORF15 isoform interacts with the multifunctional molecular chaperone NPM. NPM is a 40 kDa phosphoprotein, which is present in nucleoli and centrosomes at different stages of the cell cycle. In both these locations, protein crowding is significant, and NPM may facilitate specific interactions or prevent protein aggregation and denaturation (31
,36
38
). It is a member of the nucleoplasmin family of chaperones and has a number of apparently distinct functions, including association with pre-ribosomal particles, binding and cleavage of pre-rRNA, shuttling of ribonucleoprotein and other proteins between nucleus and cytoplasm, binding to NLS-containing proteins and interaction with p53, RB, the nucleolar protein p120, nucleolin and a number of viral proteins (36
). It is able to oligomerize, and is found as a hexamer in the nucleolus, although phosphorylated NPM may be monomeric (36
).
The interaction of RPGRORF15 and NPM and the co-localization of these two proteins at centrosomes raise the question as to the physiological significance of the interaction. NPM has been suggested to be present at centrosomes from mitosis through to late G1/S (32
). We were only able to confirm the presence of NPM at centrosomes during mitosis and specifically during metaphase (Fig. 5A). At this stage, the NPM signal overlaps with RPGRORF15 but extends beyond it, whereas RPGRORF15 is confined to the centrioles. In interphase cells, there was no clear evidence of NPM at centrosomes, whereas there was a strong nucleolar signal. At anaphase, the NPM and RPGRORF15 signals were narrowly separated, suggesting that NPM may be localized to the distal centrosomal satellites (33
) or a neighbouring structure. It is not known what proteins anchor NPM to centrosomes but the evidence presented suggests that it is not RPGRORF15, which overlaps with but does not co-localize with NPM at all stages of the cell cycle.
NPM has been proposed to licence centrosomal duplication in late G1/S phase, in co-ordination with DNA duplication, and is then released from centrosomes in response to Cdk2/cyclin E-mediated phosphorylation of Thr199 (which may be maintained by Cdk2/cyclin A during G2) (36
). NPM is thought to re-associate with centrosomes during mitosis, possibly in response to phosphorylation of Thr234 and Thr237 residues by Cdk1/cyclin B (32
). One possibility is that RPGRORF15 and RPGRIP1 associate together at the centrosomes and are involved in the unloading of microtubule transport cargoes at various stages of the cell cycle, one of which includes NPM. In this context, the recent demonstration that Ran is a core centrosomal component which can form RanGTP from RanGDP at this site (38
), raises the question as to whether the RCC1-like domain of RPGRORF15 could act as a GEF for centrosomal Ran, perhaps facilitating the unloading of NPM, which has a NLS and is capable of binding to importin. It has been shown that a number of core centrosomal proteins shuttle between the nucleus and the centrosomes, which is blocked by leptomycin (39
). These shuttling proteins are proposed to be released from importin in the presence of centrosomal RanGTP, by analogy with the unloading of importin cargoes in the nucleus (39
). This would explain the transient nature of the interaction and subsequent separation of RPGRORF15 and NPM at later stages of the cell cycle.
Vertebrate photoreceptors contain an outer segment, which is a modified sensory cilium connected to the cell body by a narrow connecting cilium. Both the RPGRORF15 and the interacting protein RPGRIP1 have been consistently localized to ciliary axonemes in all species examined (17
18
). The axoneme of connecting cilia is non-motile and projects above the basal body as a 9+0 array of microtubule doublets, corresponding to the transitional zone of motile cilia (40
), to which RPGR also localizes (18
). All phototransduction and structural proteins that are distributed to the outer segment are transported to the peri-ciliary ridge at the base of the connecting cilium (41
), which has been proposed to correspond to the transitional fibre intra-flagellar transport docking site (42
). Proteins destined for the outer segment, such as the visual pigment rhodopsin, are carried by the minus-ended microtubule-associated molecular motor cytoplasmic dynein (19
), docked in the vicinity of basal bodies and further transported into the outer segments by means of plus-end directed microtubule-associated motors such as kinesin-II (20
). Although centrioles are the equivalent structures to basal bodies in photoreceptors, it may be that RPGRORF15 plays a role in the docking of proteins at the base of the connecting cilia, as suggested by the mislocalization of opsin-containing vesicles in the Rpgr knockout mouse (15
), and is a component of a transport complex that shuttles between the inner and outer segments along the connecting cilium. The co-localization of RPGRORF15 and RPGRIP1 to basal bodies in ciliated cells is consistent with this possibility.
What is the significance of the RPGRORF15NPM interaction in a post-mitotic tissue such as retina? NPM was not seen in photoreceptor connecting cilia by immunohistochemistry, whereas strong labelling of nucleoli was evident. NPM was co-immunoprecipitated from extracts of total retina as well as both nuclear and ROS fractions. When whole retina and crude ROS fractions were examined for nuclear contamination with anti-RCC1 antibody, a weak band was present in ROS (Supplementary Material, Fig. S1E), suggesting that in post-mitotic retinal cells, the major RPGRNPM interaction occurs within nuclei. There are two possible explanations. The first is that different isoforms of RPGRORF15 (Fig. 2E) serve different roles in nuclei and centrioles/basal bodies. NPM may be common to both by acting as a chaperone for assembling protein complexes including RPGRORF15. The second possibility is that both proteins are involved in the assembly of centrosomal protein complexes within nuclei, which are subsequently exported to centrosomes, as proposed for other core centrosomal proteins, because leptomycin resulted in their nuclear retention (39
). Further work is required to establish the precise functions of RPGR and RPGRIP1 both in nuclei and in centrosomes but they join a growing number of centrosomal proteins implicated in human disease (43
46
).
| MATERIALS AND METHODS |
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Generation of anti-RPGRORF15 antibodies
Polyclonal antibodies were raised in rabbits against the bovine ORF15C2 domain (anti-bORF15C2) (18
Protein alignment
The sequences of ORF15C2 from gorilla, rhesus monkey and marmoset, cat, rat, hamster, pig and sheep were cloned by PCR using two degenerate primers (forward: 5'-ATM CCA GAG GAR MAG GAA; reverse: 5'-CTT CAA TTC CAR RTA AWG TGG YAA. M=A|C, R=A|G, W=A|T, Y=C|T). PCR products were ligated into TOPO-TA vector (Invitrogen) and sequenced with T3 primer. The sequences of ORF15 C terminal from other species were available at NCBI (http://www.ncbi.nih.gov/). Alignment of these sequences with human ORF15CT was performed using CLUSTALW tool available at the European Bioinformatics Institute (http://www.ebi.ac.uk).
Constructs
GST and EGFP fusion constructs were made using the C-terminal 81 and 83 amino acids of bovine and human RPGRORF15 in pGEX 4T3 or pGEX 4T1 (GST tag, Amersham Pharmacia Biotech) or EGFP-C1 (Clontech), respectively. Bacterial expression was induced with IPTG at 25°C and the supernatant purified with 50% slurry of glutathioneSepharose 4B beads. Human NPM was expressed in pBAD-TOPO (His tag, Invitrogen) and expression induced with 0.002% arabinose at 25°C.
Yeast two-hybrid analysis
The human ORF15C2 construct was inserted into the pAS vector (Clontech) and transformed into the Y190 yeast strain (Yeast protocols Handbook PT3024-1). Human NPM was inserted into the pACT vector (Clontech). A colour assay for ß-galactosidase activity with chlorophenol red ß-D-galactopyranoside was carried out as described (Clontech Yeast Protocols Handbook PT3024-1).
Preparation of ROS extracts
Bovine retinal fractions enriched in ROS were prepared using modifications to the method of Papermaster and Dreyer (47
). Briefly, one bovine retina was suspended in 1.0 ml sucrose homogenizing medium (34% sucrose, 65 mM NaCl, 2 mM MgCl2, 5 mM Trisacetate, pH 7.4) and shaken for 1 min. The resulting suspension was centrifuged at 1800g for 4 min and the supernatant removed into two volumes 10 mM Trisacetate, pH 7.4. The pellet was resuspended in 1.0 ml sucrose homogenizing medium and homogenized with a loose fitting pestle, four to five passes on ice. The suspension was centrifuged at 1800g for 4 min, the supernatant removed into two volumes of 10 mM Trisacetate pH 7.4 and pooled with the first supernatant. The pooled supernatants were centrifuged at 2600g for 4 min and the resulting pellet was designated the crude ROS extract.
Pull-down assays
The GSTORF15C2 (bovine) protein was used to pull down interacting proteins from bovine retina extracts after overnight incubation at 4°C. One bovine retina (250 mg) and 250 mg bovine kidney were homogenized on ice using a Dounce homogenizer in phosphate buffered saline (PBS) containing 2% Triton X-100 and protease inhibitors and incubated by rotating at room temperature for 30 min. Tissues were further lysed by several rounds of freeze/thaw and sonication and the large debris removed by centrifugation at 10 000g for 20 min. The soluble supernatant was divided into two equal aliquots, one of which was incubated with bovine GSTORF15C2 and the other with the GST-only vector control, each immobilized on glutathioneSepharose 4B beads. Bound proteins were washed and removed by boiling, then separated by SDSPAGE. Excised bands that were absent from GST-only control pull-downs were digested in situ with trypsin and identified by MALDI-TOF mass spectrometry or anti-NPM antibody by western blots.
In other experiments, sonicated HeLa cell extract supernatant was incubated at 4°C overnight with human and bovine EGFPORF15C2, washed with PBS and purified on glutathioneSepharose 4B beads prior to analysis by SDSPAGE and western blotting with anti-NPM. Recombinant human NPM was also incubated with human GSTORF15C2 and analysed as described earlier. In SDSPAGE gels, 10 µl input extract was loaded and 200 µl used for each of the ORF15C2 and control pull downs.
Protein identification by mass spectrometry
Identification of NPM by peptide mass mapping utilized methods described in detail elsewhere (48
,49
). Briefly, gel bands were excised, destained and digested in-gel with trypsin and the resulting peptides extracted for analysis with a Voyager DE Pro MALDI-TOF mass spectrometer (PE Biosystems, Framingham, MA, USA). Measured peptide masses were used to query the Swiss-Protein, TrEMBL and NCBI sequence databases for matches using MS-Fit and Profound search programs.
Co-immunoprecipitation from cells transfected with EGFPhORF15C2
Human ORF15C2, subcloned in the pEGFP vector (Clontech), and pEGFP vector control were transfected into HeLa cells using FuGENE 6 (Roche). After 3 days, the transfected HeLa cells were lysed, and anti-EGFP antibody and protein A beads were added to the lysed supernantant and incubated at 4°C overnight then washed with PBS. After boiling, the extract was subjected to SDSPAGE followed by immunoblotting with antibody (Supplementary Material, Fig. S1G).
Co-immunoprecipitation from bovine RNE
Nuclear extracts were prepared from bovine retina and used for co-immunoprecipitation experiments as described previously (50
,51
). The immunoprecipitates were subjected to SDSPAGE followed by immunoblot analysis with appropriate antibodies. The immunoblots were developed using the enhanced chemiluminescence kit (Pierce, New York, NY, USA).
Immunoblot analysis of the bovine RNE with ORF15CP and ORF15C2 antibodies
Bovine retinal whole cell extract and nuclear extract (100200 µg each) were subjected to SDSPAGE followed by immunoblotting using anti-ORF15CP or anti-ORF15C2 antibody. Equal amounts of protein were run on 7.5% (for ORF15 analysis) or 10% (all other antibodies) SDSPAGE gels and transferred to nitrocellulose membrane. Membranes were blocked in 5% non-fat dried milk in PBS. Primary antibodies were used at 1:100 [anti-ORF15 and anti-RCC1 (BD Biosciences)] or 1:2000 for anti-NPM (a gift from Dr P.K. Chan, Chinese University of Hong Kong). Anti-rabbit (BioRad) or anti-mouse (Scottish Antibody Production Unit) HRP-conjugated secondary antibodies were used at a 1:5000 dilution. Bound antibody was visualized by ECL (Amersham Biosciences).
RTPCR of RPGRORF15
Total RNA from cultured cells was isolated using the Micro-to-midi total RNA purification system (Invitrogen). RTPCR was performed with the SuperScriptTM one-step RTPCR kit (Invitrogen). The following primers were used: RPGRORF15, 5'-GAT TCT TTT TCA ATG AGG AGA ACA -3' and 5'-ATT TCC TTT TGA ATC CTC TGC TCC-3'; glyceraldehyde-3-phosphate dehydrogenase (GAPD) 5'-ATG GGG AAG GTG AAG GTC GGA-3' and 5'-TTA CTC CTT GGA GGC CAT GTG-3'. The forward primer for RPGR is in exon 11, the reverse primer is near the start of exon ORF15, which results in an RTPCR product of
498 bp.
Cells and transfection
COS7 cells were maintained in Dulbecco's modified Eagle medium (DMEM) supplemented with 5% fetal calf serum, penicillin (100 U/ml) and streptomycin (130 µg/ml) at 37°C in an atmosphere of 5% CO2. Transient transfection was performed using FuGENE 6 (Roche) (6 µl) added to DNA (2.0 µg) following the manufacturer's instructions. Cells were transfected with an enhanced green fluorescent protein (EGFP) vector containing the ORF15C2 DNA sequence fused to the C-terminus of EGFP. After incubation for 48 h, cells were washed in PBS, fixed with ice cold methanol for 2 min at 20°C, washed in PBS, blocked with 10% normal sheep serum in PBS, then incubated with anti-NPM at 1:100 in 10% normal sheep serum for 1 h at room temperature, in a moist chamber. Cells were washed in PBS, blocked again and incubated with Texas Red-conjugated secondary antibody (Jackson Laboratories) at 1:100 in 10% normal sheep serum in PBS for 1 h at room temperature in the dark, in a moist chamber. Cells were then washed in PBS and mounted in Vectashield (Vector Laboratories Ltd) containing 4'-6-diamidino-2-phenylindole (DAPI) (1.0 µg/ml). Images were captured using an Axioplan two fluorescent microscope and analysed using IPLab software.
Mouse internal IMCD3 were purchased from American Type Culture Collection (Rockville, MD, USA) and cultured to confluence in DMEM/HAM's F12 (Gibco-BRL, Rockville, MD, USA) and supplemented with 10% fetal bovine serum (FBS) and 100 U/ml of penicillin/streptomycin in a humidified 5% CO2 incubator, maintained at 37°C.
Immunocytochemistry
COS7 cells were grown at 37°C in a 5% CO2 atmosphere in DMEM supplemented with 10% FBS and penicillinstreptomycin (100 IU/ml and 100 µg/ml, respectively). For immunofluorescence, cells were grown on acid treated coverslips overnight before being fixed and permeabilized with 20°C methanol for 10 min. The cells were rehydrated with PBS for 10 min then blocked in PBS1% BSA for 5 min. Cells were then incubated with the anti-ORF15C2 antibody (1:50, rabbit) plus anti-
-tubulin (1:2000; Sigma, St Louis, MO, USA). The mouse primary antibodies were detected using biotin anti-mouse (Amersham) followed by incubation with Streptavidin Texas Red to detect the biotin (Amersham). The rabbit primary antibodies were detected using Alexa 488 (Molecular probes, Eugene, OR, USA) and the DNA was stained using Hoechst 33258 dye (Calbiochem, 0.2 µg/ml) for 1 min. All antibodies were diluted in PBS3% BSA and all antibody incubations were for 45 min at room temperature. The cells were washed 3x5 min between each antibody incubation. Following the completion of labelling, the coverslips were mounted onto slides in 80% glycerol 3% n-propylgallate to prevent fading. Images were captured on a Nikon TE300 inverted microscope using an ORCA ER (Hamamatsu, Shizuoka, Japan) using Openlab 3.09 software (Improvision, Coventry, UK) and processing using Adobe Photoshop (Adobe Systems, San Jose, CA, USA).
Fluorescence staining of retinal cryosections
Immunofluorescence studies were essentially performed as previously described (52
,53
). Briefly, eyes from adult C57BL/6J mice were prefixed in 4% paraformaldehyde in PBS for 1 h at room temperature, washed, soaked with 30% sucrose in PBS overnight, and cryofixed in melting iso-pentane. Cryosections were placed on poly-L-lysine-precoated coverslips. Specimens were incubated with 50 mM NH4Cl and 0.1% Tween-20 in PBS and blocked with blocking solution [0.5% cold-water fish gelatin (Sigma) plus 0.1% ovalbumin (Sigma) in PBS]. For double labelling, sections were incubated with a mixture of antibodies in blocking solution overnight at 4°C. In these experiments, anti-centrin antibodies were used as markers for the connecting cilium (54
). The specimens were washed and subsequently incubated with secondary antibodies conjugated to Alexa® 488 or Alexa® 546 (Molecular Probes) in blocking solution for 1 h at room temperature in the dark. Washed sections were mounted in Mowiol 4.88 (Hoechst, Frankfurt, Germany) containing 2% n-propyl-gallate, and in the case of triple staining, 1 µg/ml 4,6-diamidino-2-phenylindole. Mounted retinal sections were examined with a Leica DMRP microscope. Images were obtained with a Hamamatsu Orca ER CCD camera (Hamamatsu city, Japan) and processed with Adobe Photoshop (Adobe Systems).
| SUPPLEMENTARY MATERIAL |
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Supplementary Material is available at HMG Online.
| ACKNOWLEDGEMENTS |
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We are grateful to Dr Tiansen Li (Harvard) for an RPGRIP1 antibody and for providing Rpgr knockout mice. We thank S. Bruce for the artwork. We acknowledge the support of the Medical Research Council (A.F.W.), Foundation Fighting Blindness (A.F.W., A.S. and J.W.C.), NIH EY006603 and EY014239 (J.W.C.), EY007961, EY007003 (A.S.), Wellcome Trust, BBSRC and AICR (A.M.F.), Research to Prevent Blindness (A.S.) and British Retinitis Pigmentosa Society (A.F.W.). A.S. is Harold F. Falls Collegiate Professor and RPB Senior Scientific Investigator and A.M.F. is a Lister Institute Research Fellow.
| FOOTNOTES |
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Present address: Centre for Molecular Medicine, The University of Manchester, Oxford Road, Manchester M13 9PT, UK. | REFERENCES |
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