Identification of novel molecular components of the photoreceptor connecting cilium by immunoscreens

Cilia - The sensory antennae in the eye

Cilia are hair-like projections found on almost all cells in the human body. Originally believed to function merely in motility, the function of solitary non-motile (primary) cilia was long overlooked. Recent research has demonstrated that primary cilia function as signalling hubs that sense environmental cues and are pivotal for organ development and function, tissue hoemoestasis, and maintenance of human health. Cilia share a common anatomy and their diverse functional features are achieved by evolutionarily conserved functional modules, organized into sub-compartments. Defects in these functional modules are responsible for a rapidly growing list of human diseases collectively termed ciliopathies. Ocular pathogenesis is common in virtually all classes of syndromic ciliopathies, and disruptions in cilia genes have been found to be causative in a growing number of non-syndromic retinal dystrophies. This review will address what is currently known about cilia contribution to visual function. We will focus on the molecular and cellular functions of ciliary proteins and their role in the photoreceptor sensory cilia and their visual phenotypes. We also highlight other ciliated cell types in tissues of the eye (e.g. lens, RPE and Müller glia cells) discussing their possible contribution to disease progression. Progress in basic research on the cilia function in the eye is paving the way for therapeutic options for retinal ciliopathies. In the final section we describe the latest advancements in gene therapy, read-through of non-sense mutations and stem cell therapy, all being adopted to treat cilia dysfunction in the retina.

The Leber congenital amaurosis protein AIPL1 and EB proteins co-localize at the photoreceptor cilium

Purpose

The aim of this study was to investigate the interaction and co-localization of novel interacting proteins with the Leber congenital amaurosis (LCA) associated protein aryl hydrocarbon receptor interacting protein-like 1 (AIPL1).

Methods

The CytoTrapXR yeast two-hybrid system was used to screen a bovine retinal cDNA library. A novel interaction between AIPL1 and members of the family of EB proteins was confirmed by directed yeast two-hybrid analysis and co-immunoprecipitation assays. The localization of AIPL1 and the EB proteins in cultured cells and in retinal cryosections was examined by immunofluorescence microscopy and cryo-immunogold electron microscopy.

Results

Yeast two-hybrid (Y2H) analysis identified the interaction between AIPL1 and the EB proteins, EB1 and EB3. EB1 and EB3 were specifically co-immunoprecipitated with AIPL1 from SK-N-SH neuroblastoma cells. In directed 1:1 Y2H analysis, the interaction of EB1 with AIPL1 harbouring the LCA-causing mutations A197P, C239R and W278X was severely compromised. Immunofluorescent confocal microscopy revealed that AIPL1 did not co-localize with endogenous EB1 at the tips of microtubules, endogenous EB1 at the microtubule organising centre following disruption of the microtubule network, or with endogenous β-tubulin. Moreover, AIPL1 did not localize to primary cilia in ARPE-19 cells, whereas EB1 co-localized with the centrosomal marker pericentrin at the base of primary cilia. However, both AIPL1 and the EB proteins, EB1 and EB3, co-localized with centrin-3 in the connecting cilium of photoreceptor cells. Cryo-immunogold electron microscopy confirmed the co-localization of AIPL1 and EB1 in the connecting cilia in human retinal photoreceptors.

Conclusions

AIPL1 and the EB proteins, EB1 and EB3, localize at the connecting cilia of retinal photoreceptor cells, but do not co-localize in the cellular microtubule network or in primary cilia in non-retinal cells. These findings suggest that AIPL1 function in these cells is not related to the role of EB proteins in microtubule dynamics or primary ciliogenesis, but that their association may be related to a specific role in the specialized cilia apparatus of retinal photoreceptors.

Isotope coded protein labeling coupled immunoprecipitation (ICPL-IP): a novel approach for quantitative protein complex analysis from native tissue

High confidence definition of protein interactions is an important objective toward the understanding of biological systems. Isotope labeling in combination with affinity-based isolation of protein complexes has increased in accuracy and reproducibility, yet, larger organisms--including humans--are hardly accessible to metabolic labeling and thus, a major limitation has been its restriction to small animals, cell lines, and yeast. As composition as well as the stoichiometry of protein complexes can significantly differ in primary tissues, there is a great demand for methods capable to combine the selectivity of affinity-based isolation as well as the accuracy and reproducibility of isotope-based labeling with its application toward analysis of protein interactions from intact tissue. Toward this goal, we combined isotope coded protein labeling (ICPL)(1) with immunoprecipitation (IP) and quantitative mass spectrometry (MS). ICPL-IP allows sensitive and accurate analysis of protein interactions from primary tissue. We applied ICPL-IP to immuno-isolate protein complexes from bovine retinal tissue. Protein complexes of immunoprecipitated β-tubulin, a highly abundant protein with known interactors as well as the lowly expressed small GTPase RhoA were analyzed. The results of both analyses demonstrate sensitive and selective identification of known as well as new protein interactions by our method.

Methods for the isolation of sensory and primary cilia--an overview

Detailed proteomic analyses of mammalian olfactory and rod photoreceptor sensory cilia are now available, providing an inventory of resident ciliary proteins and laying the foundation for future studies of developmental and spatiotemporal changes in the composition of sensory cilia. Cilia purification methods that were elaborated and perfected over several decades were essential for these advances. In contrast, the proteome of primary cilia is yet to be established, because purification procedures for this organelle have been developed only recently. In this chapter, we review current techniques for the purification of olfactory and photoreceptor cilia, and evaluate methods designed for the selective isolation of primary cilia.

Gardner's syndrome (familial adenomatous polyposis): a cilia-related disorder

Familial adenomatous polyposis (FAP) is an autosomal dominant form of intestinal polyposis and colorectal cancer caused by germ-line mutations in the adenomatous polyposis coli (APC) gene. The term Gardner's syndrome is used to describe extracolonic manifestations, such as osteomas, skin cysts, congenital hypertrophy of the retinal pigmented epithelium (CHRPE), and desmoid tumours (aggressive fibromatosis), that are especially prominent in families with FAP. We postulate that a ciliary dysfunction is the underlying pathogenetic mechanism of extraintestinal manifestations in patients with FAP. This postulation is based on the presence of common clinical manifestations (ie, cysts, retinal abnormalities, and fibrosis) in Gardner's syndrome and cilia-related disorders. Additionally, both APC and the cilia have degradation of beta-catenin as the common downstream target in the Wnt-signalling pathway. Mutations in APC causing Gardner's syndrome are clustered in a region encoding a series of amino-acid repeats responsible for the binding to beta-catenin. Proofs of principle that beta-catenin could be the key mediator of the ciliary disorder also rely in the findings that overexpression of beta-catenin induces polycystic kidney disease, and CHRPE phenotypes in animal models. Other candidates for the common link between Gardner's syndrome and cilia-related disorders are the APC-binding proteins: end-binding protein 1 (EB1) and kinesin-family-member 3a (KIF3a), both of which are ciliary proteins involved in intraflagellar transport. Finally, pathogenetic similarities between some ciliopathies and extraintestinal tumours in FAP suggest a cilia defect. Understanding extracolonic manifestations in the context of FAP as a ciliary disorder might add new therapeutic options for patients with Gardner's syndrome.

Centrins in retinal photoreceptor cells: regulators in the connecting cilium

Changes in the intracellular Ca2+ concentration regulate the visual signal transduction cascade directly or more often indirectly through Ca2+-binding proteins. Here we focus on centrins, which are members of a highly conserved subgroup of the EF-hand superfamily of Ca2+-binding proteins in photoreceptor cells of the vertebrate retina. Centrins are commonly associated with centrosome-related structures. In mammalian retinal photoreceptor cells, four centrin isoforms are expressed as prominent components in the connecting cilium linking the light-sensitive outer segment compartment with the metabolically active inner segment compartment. Our data indicate that Ca2+-activated centrin isoforms assemble into protein complexes with the visual heterotrimeric G-protein transducin. This interaction of centrins with transducin is mediated by binding to the betagamma-dimer of the heterotrimeric G-protein. More recent findings show that these interactions of centrins with transducin are reciprocally regulated via site-specific phosphorylations mediated by the protein kinase CK2. The assembly of centrin/G-protein complexes is a novel aspect of translocation regulation of signalling proteins in sensory cells, and represents a potential link between molecular trafficking and signal transduction in general.

SANS (USH1G) expression in developing and mature mammalian retina

The human Usher syndrome (USH) is the most common form of combined deaf-blindness. Usher type I (USH1), the most severe form, is characterized by profound congenital deafness, constant vestibular dysfunction and prepubertal-onset of retinitis pigmentosa. Five corresponding genes of the six USH1 genes have been cloned so far. The USH1G gene encodes the SANS (scaffold protein containing ankyrin repeats and SAM domain) protein which consists of protein motifs known to mediate protein-protein interactions. Recent studies indicated SANS function as a scaffold protein in the protein interactome related to USH. Here, we generated specific antibodies for SANS protein expression analyses. Our study revealed SANS protein expression in NIH3T3 fibroblasts, murine tissues containing ciliated cells and in mature and developing mammalian retinas. In mature retinas, SANS was localized in inner and outer plexiform retinal layers, and in the photoreceptor cell layer. Subcellular fractionations, tangential cryosections and immunocytochemistry revealed SANS in synaptic terminals, cell-cell adhesions of the outer limiting membrane and ciliary apparati of photoreceptor cells. Analyses of postnatal developmental stages of murine retinas demonstrated SANS localization in differentiating ciliary apparati and in fully developed cilia, synapses, and cell-cell adhesions of photoreceptor cells. Present data provide evidence that SANS functions as a scaffold protein in USH protein networks during ciliogenesis, at the mature ciliary apparatus, the ribbon synapse and the cell-cell adhesion of mammalian photoreceptor cells. Defects of SANS may cause dysfunction of the entire network leading to retinal degeneration, the ocular symptom characteristic for USH patients.

Protein networks and complexes in photoreceptor cilia

Vertebrate photoreceptor cells are ciliated sensory cells specialized for single photon detection. The photoreceptor outer segment corresponds to the ciliary shaft of a prototypic cilium. In the outer segment compartment, the ciliary membrane is highly modified into membranous disks which are enveloped by the plasma membrane in rod cells. At these outer segment disks, the visual transduction cascade--a prototypical G-protein coupled receptor transduction pathway is arranged. The light sensitive outer segments are linked by the socalled connecting cilium with the inner segment, the photoreceptor compartment which contains all organelles necessary for cell metabolism. The connecting cilium correlates with the transition zone, the short junction between the basal body and the axoneme of a prototypic cilium. The connecting cilium and the calycal processes, including the periciliary ridge complex, as well as the basal body complex are in close functional association with each other. In the latter ciliary compartments, the export and import from/into the outer segment of the photoreceptor cell are controlled and regulated. In all subciliary compartments, proteins are arranged in functional multiprotein complexes. In the outer segment, signaling components are arranged into complexes which provide specificity and speed for the signaling and serve in adaptation. Centrin-G-protein complexes may regulate the light driven translocation of the visual G-protein transducin through the connecting cilium. Intraflagellar transport (IFT) complexes may serve in intersegmental exchange of molecules. The import/export of molecules is thought to be regulated by proteins arranged in networks at the basal body complex. Proteins of the interactome related to the human Usher syndrome are localized in the connecting cilium and may participate in the ciliary transport, but are also arranged at interfaces between the inner segment and the connecting cilium where they probably control the cargo handover between the transport systems of the inner segment and these of the cilium. Furthermore, USH protein complexes may further provide mechanical stabilization to membrane specializations of the calycal processes and the connecting cilium. The protein complex in which the retinitis pigmentosa GTPase regulator (RPGR) participates in the ciliary compartments also plays a key role in the function and maintenance of photoreceptor cells. It further associates through the presumed scaffolding protein RPGRIP1 with the nephrocystin protein network. Although many of these proteins have been also found in prototypic cilia or primary cilia, the arrangements of the proteins in complexes can be specific for vertebrate photoreceptor cells. Defects of proteins in these complexes lead to photoreceptor cell death and retinal degeneration, underlying syndromic and non-syndromic blindness.

The proteome of the mouse photoreceptor sensory cilium complex

Primary cilia play critical roles in many aspects of biology. Specialized versions of primary cilia are involved in many aspects of sensation. The single photoreceptor sensory cilium (PSC) or outer segment elaborated by each rod and cone photoreceptor cell of the retina is a classic example. Mutations in genes that encode cilia components are common causes of disease, including retinal degenerations. The protein components of mammalian primary and sensory cilia have not been defined previously. Here we report a detailed proteomics analysis of the mouse PSC complex. The PSC complex comprises the outer segment and its cytoskeleton, including the axoneme, basal body, and ciliary rootlet, which extends into the inner segment of photoreceptor cells. The PSC complex proteome contains 1968 proteins represented by three or more unique peptides, including approximately 1500 proteins not detected in cilia from lower organisms. This includes 105 hypothetical proteins and 60 proteins encoded by genes that map within the critical intervals for 23 inherited cilia-related disorders, increasing their priority as candidate genes. The PSC complex proteome also contains many cilia proteins not identified previously in photoreceptors, including 13 proteins produced by genes that harbor mutations that cause cilia disease and seven intraflagellar transport proteins. Analyses of PSC complexes from rootletin knock-out mice, which lack ciliary rootlets, confirmed that 1185 of the identified PSC complex proteins are derived from the outer segment. The mass spectrometry data, benchmarked by 15 well characterized outer segment proteins, were used to quantify the copy number of each protein in a mouse rod outer segment. These results reveal mammalian cilia to be several times more complex than the cilia of unicellular organisms and open novel avenues for studies of how cilia are built and maintained and how these processes are disrupted in human disease.

Centrins, gatekeepers for the light-dependent translocation of transducin through the photoreceptor cell connecting cilium

Centrins are members of a highly conserved subgroup of the EF-hand superfamily of Ca(2+)-binding proteins commonly associated with centrosome-related structures. In the retina, centrins are also prominent components of the photoreceptor cell ciliary apparatus. Centrin isoforms are differentially localized at the basal body and in the lumen of the connecting cilium. All molecular exchanges between the inner and outer segments occur through this narrow connecting cilium. Ca(2+)-activated centrin isoforms bind to the visual heterotrimeric G-protein transducin via an interaction with the betagamma-subunit. Ca(2+)-dependent assemblies of centrin/G-protein complexes may regulate the transducin movement through the connecting cilium. Formation of this complex represents a novel mechanism in regulation of translocation of signaling proteins in sensory cells, as well as a potential link between molecular trafficking and signal transduction in general.

The Microtubule Plus End-Tracking Protein EB1 Is Localized to the Flagellar Tip and Basal Bodies in Chlamydomonas reinhardtii

Flagellar axonemes assemble and continuously turn over at the flagellar tip. The supply and removal of axonemal subunits at the tip are mediated by intraflagellar transport (IFT), a motility process essential for the assembly and maintenance of all eukaryotic flagella and cilia. IFT is characterized by the movement of large protein complexes (IFT particles) from the basal bodies to the flagellar tip by kinesin-II and from the tip back to the basal bodies by cytoplasmic dynein 1b. The IFT particles consist of approximately 16 polypeptides partitioned into two complexes, A and B, and associate with axonemal precursors/turn over products. The mechanisms by which IFT motor regulation and cargo loading/unloading occur at the flagellar tip are unknown. We identified a Chlamydomonas reinhardtii ortholog of the microtubule (MT) plus end-tracking protein EB1 [4] (CrEB1) and show here that CrEB1 localizes to the tip of flagella and to the proximal part of the basal bodies. Furthermore, we found that CrEB1 is depleted from flagella of the temperature-sensitive (ts) flagellar assembly-defective (fla) mutant fla11(ts) at the restrictive temperature. This depletion of CrEB1 is accompanied by a dramatic accumulation of IFT particle polypeptides near the flagellar tip.

The retinitis pigmentosa GTPase regulator (RPGR)- interacting protein: subserving RPGR function and participating in disk morphogenesis

Retinitis pigmentosa is a photoreceptor degenerative disease leading to blindness in adulthood. Leber congenital amaurosis (LCA) describes a more severe condition with visual deficit in early childhood. Defects in the retinitis pigmentosa GTPase regulator (RPGR) and an RPGR-interacting protein (RPGRIP) are known causes of retinitis pigmentosa and LCA, respectively. Both proteins localize in the photoreceptor connecting cilium (CC), a thin bridge linking the cell body and the light-sensing outer segment. We show that RPGR is absent in the CC of photoreceptors lacking RPGRIP, but not vice versa. Mice lacking RPGRIP elaborate grossly oversized outer segment disks resembling a cytochalasin D-induced defect and have a more severe disease than mice lacking RPGR. Mice lacking both proteins are phenotypically indistinguishable from mice lacking RPGRIP alone. In vitro, RPGRIP forms homodimer and elongated filaments via interactions involving its coiled-coil and C-terminal domains. We conclude that RPGRIP is a stable polymer in the CC where it tethers RPGR and that RPGR depends on RPGRIP for subcellular localization and normal function. Our data suggest that RPGRIP is also required for disk morphogenesis, putatively by regulating actin cytoskeleton dynamics. The latter hypothesis may be consistent with a distant homology between the C-terminal domain of RPGRIP and an actin-fragmin kinase, predicted by fold recognition algorithms. A defect in RPGRIP encompasses loss of both functions, hence the more severe clinical manifestation as LCA.