Transition Zone Proteins Research Articles

Subdiffraction Imaging Reveals Molecular Architecture at the Transition Zone of Primary Cilia

Recent studies have identified important regulating elements for transition zone (TZ) gating in cilia. However, the architecture of the TZ region and its arrangement relative to intraflagellar transport (IFT) proteins remain largely unknown, hindering the mechanistic understanding of the regulation mechanisms. One of the major challenges comes from the tiny volume at the ciliary base packed with numerous proteins, with the diameter of the TZ close to the diffraction limit of conventional microscopes. Using a custom-built stimulated emission depletion (STED) superresolution microscope, we revealed relative localizations of TZ proteins, IFT proteins, transition fiber (TF) proteins, and centriole proteins. We found TCTN2 at the outmost periphery of the TZ close to the ciliary membrane, with a 227±18 nm diameter. TMEM67 was adjacent to TCTN2, with a 205±20 nm diameter. RPGRIP1L was localized toward the axoneme at the same axial level as TCTN2 and TMEM67, with a 165±8 nm diameter. Surprisingly, CEP290 (antibody against C-terminal amino acids) was localized at the proximal side of the TZ close to the distal end of the centrin-labeled basal body. The lateral width was unexpectedly close to the width of the basal body, distant from the potential Y-links region of the TZ. IFT88 was also surprisingly distributed in two distinct patterns, forming three puncta or a Y shape at the ciliary base. We hypothesize that the two distribution states of IFT88 correspond to the open and closed gating states of the TZ, where IFT particles aggregate to form three puncta when the gate is closed, and move to form the branches of the Y-shape pattern when the gate is open.

Ciliopathy proteins establish a bipartite signaling compartment in a C. elegans thermosensory neuron.

How signaling domains form is an important, yet largely unexplored question. Here, we show that ciliary proteins help establish two contiguous, yet distinct cyclic GMP (cGMP) signaling compartments in Caenorhabditis elegans thermosensory AFD neurons. One compartment, a bona fide cilium, is delineated by proteins associated with Bardet-Biedl syndrome (BBS), Meckel syndrome and nephronophthisis at its base, and requires NPHP-2 (known as inversin in mammals) to anchor a cGMP-gated ion channel within the proximal ciliary region. The other, a subcompartment with profuse microvilli and a different lipid environment, is separated from the dendrite by a cellular junction and requires BBS-8 and DAF-25 (known as Ankmy2 in mammals) for correct localization of guanylyl cyclases needed for thermosensation. Consistent with a requirement for a membrane diffusion barrier at the subcompartment base, we reveal the unexpected presence of ciliary transition zone proteins where no canonical transition zone ultrastructure exists. We propose that differential compartmentalization of signal transduction components by ciliary proteins is important for the functions of ciliated sensory neurons.

The AmAZI1ng Roles of Centriolar Satellites during Development

The precise trafficking and spatial organization of signaling molecules within cells is critical for many fundamental cellular processes. Two interconnected microtubule-based organelles, the centrosome and primary cilium, have been making headlines recently due to their role as central “hubs” for coordinating such signaling events. The centrosome is the major microtubule-nucleating center in animal cells, which polarizes microtubule arrays and thereby directs microtubule-based trafficking toward itself and its associated structure, the primary cilium. [1]. The primary cilium is a tiny hair-like sensory organelle that is templated by one of two centrioles, core elements of the centrosome, and protrudes above the apical surface of almost every cell in the human body (Figure 1). Together, the centrosome and cilium mediate the initiation and transmission of extracellular signals to the interior of the cell, thus controlling many aspects of cell physiology [2], [3]. Defects in the structure and/or function of these organelles result in human disease conditions termed “ciliopathies,” a heterogeneous group of disorders with phenotypes including cystic kidneys; digit, bone, and brain anomalies; infertility; and even cancer [4], [5].

Cell- and subunit-specific mechanisms of CNG channel ciliary trafficking and localization inC. elegans

Primary cilia are ubiquitous sensory organelles that concentrate transmembrane signaling proteins essential for sensing environmental cues. Mislocalization of crucial ciliary signaling proteins, such as the tetrameric cyclic nucleotide-gated (CNG) channels, can lead to cellular dysfunction and disease. Although several cis- and trans-acting factors required for ciliary protein trafficking and localization have been identified, whether these mechanisms act in a protein- and cell-specific manner is largely unknown. Here, we show that CNG channel subunits can be localized to discrete ciliary compartments in individual sensory neurons in C. elegans, suggesting that channel composition is heterogeneous across the cilium. We demonstrate that ciliary localization of CNG channel subunits is interdependent on different channel subunits in specific cells, and identify sequences required for efficient ciliary targeting and localization of the TAX-2 CNGB and TAX-4 CNGA subunits. Using a candidate gene approach, we show that Inversin, transition zone proteins, intraflagellar transport motors and a MYND-domain protein are required to traffic and/or localize CNG channel subunits in both a cell- and channel subunit-specific manner. We further find that TAX-2 and TAX-4 are relatively immobile in specific sensory cilia subcompartments, suggesting that these proteins undergo minimal turnover in these domains in mature cilia. Our results uncover unexpected diversity in the mechanisms that traffic and localize CNG channel subunits to cilia both within and across cell types, highlighting the essential contribution of this process to cellular functions.

NPHP and MKS proteins and the ciliary transition zone

The cilium has emerged as an important signaling and sensory organelle needed for mammalian development and adult tissue homeostasis. It mediates these effects by locating specific receptors, channels, and other signaling factors needed for pathway regulation along the cilium membrane and axoneme. To establish the cilia signaling complement of proteins distinct from that of the cytosol or cell membrane there is a domain called the transition zone (TZ) located at the base that is believed to function as a diffusion barrier, restricting protein entry or exit from the cilium. The structure of the TZ has been well defined through EM analysis, but the proteins required to generate the TZ are only now being identified. Using C. elegans models, we have shown that many of the proteins involved in human ciliopathies such as Meckel Gruber syndrome (MKS) and Nephronophthisis (NPHP) grossly localize to the TZ. We are currently defining where these proteins localize on structures within the TZ using higher resolution EM approaches. Further, the NPHP and MKS proteins form two genetically interacting complexes in C. elegans that when disrupted result in the loss of structures in the TZ, inappropriate ciliary localization of nonciliary proteins, and severe cilia assembly/positioning defects. Based on the synthetic cilia phenotype observed in all mks;nphp double mutants that we generated thus far, we conducted an EMS enhancer screen using nphp-4 single mutants. The goal of the screen was to generate secondary mutations that would genetically interact with the initial nphp-4 mutation. Our prediction is that this would yield novel mutations in proteins that function with the MKS or NPHP complexes and would thus provide ideal candidates for novel loci involved in human ciliopathies patients. Using whole genome sequence analysis, we have begun identifying the affected genes. As predicted, three of the alleles were in known MKS genes. Several other mutations in cilia genes have been identified but have not previously been associated with either NPHP or MKS. The role of these genes and the interaction with the NPHP and MKS complexes are being further explored in both C. elegans and mouse models. Understanding how the TZ forms and how mutations in TZ proteins disrupt the diffusion barrier will provide important insights into the ciliopathies and how this organelle serves its diverse signaling and sensory functions.

Live imaging of Rab8 trafficking defects in cc2d2a mutant zebrafish

Primary cilia provide a means of regulating and concentrating receptors and other proteins essential for transmission of sensory signals or signaling pathways. Consequently, a thorough understanding of the sorting and trafficking mechanisms that allow appropriate protein delivery to the ciliary compartment is crucial to our understanding of ciliary function in development, homeostasis and disease. Recent work has demonstrated that ciliopathy proteins, such as CC2D2A, are localized to the transition zone at the base of the cilium and function to regulate protein entry into the ciliary compartment. Upstream of the cilium, small GTPases from the Rab family participate in controlling trafficking of ciliary-directed proteins. Here, we describe the relationship between the transition zone protein Cc2d2a and Rab8 trafficking in photoreceptors. Detailed phenotypic analysis of a zebrafish cc2d2a mutant reveals typical ciliopathy phenotypes including cystic kidneys and abnormal photoreceptor outer segments. Mislocalization of opsins in mutant photoreceptors and massive accumulation of vesicles suggest a role for Cc2d2a in vesicle trafficking. Partial rab8 knockdown enhances the photoreceptor phenotype of cc2d2a mutants. A fluorescently-tagged Rab8 transgene demonstrates a punctate localization pattern for Rab8 in photoreceptors that is disrupted in the absence of Cc2d2a. Live imaging of Rab8 trafficking in zebrafish photoreceptors reveals complex and highly dynamic movements of Rab8 puncta towards different cellular destinations, including the outer segment and the synapse, which are differentially affected by loss of Cc2d2a function.

Functional analysis of the transition zone protein Rpgrip1l during zebrafish development

We investigated the function of Rpgrip1l during zebrafish development. Rpgrip1l encodes a protein localised at the ciliary transition zone and interacts functionally with NPH and MKS for the formation and function of the ciliary gate. The human RPGRIP1L gene is a causal gene in Meckel and Joubert type B syndromes, characterised by polydactyly, kidney cysts and central nervous system malformations. Using morpholinos injection, we show that loss of Rpgrip1l function leads to several early phenotypes such as convergent-extension phenotype, randomisation of left-right asymmetry and hydrocephaly. We focussed our study on the Wnt-PCP defects and we demonstrated that in the zebrafish floorplate, Rpgrip1l is required for correct positioning of the basal body along the planar polarity axis. We confirmed Rpgrip1l function on basal body positioning in the mechanosensory hair cells of the cochlea of the murine mutant for Rpgrip1l. Our results strongly suggest that Rpgrip1l is essential for recruiting and stabilizing dishevelled, a major actor of the PCP pathway, at the basal body and/or cilium. Indeed, in two different cell types, in the zebrafish floor plate and in the murine cochlea, dishevelled proteins are enriched at the cilium and/or basal body, and this localization is severely perturbed upon Rpgrip1l depletion. Finally, we demonstrate that, in the zebrafish floor plate, the function of Rpgrip1l in basal body positioning is mediated by dishevelled. We propose that Rpgrip1l participates in a protein complex required for recruiting and stabilizing dishevelled at the cilium, a process essential for planar polarization of the basal body.

TCTN3 Mutations Cause Mohr-Majewski Syndrome

Orofaciodigital syndromes (OFDSs) consist of a group of heterogeneous disorders characterized by abnormalities in the oral cavity, face, and digits and associated phenotypic abnormalities that lead to the delineation of 13 OFDS subtypes. Here, by a combined approach of homozygozity mapping and exome ciliary sequencing, we identified truncating TCTN3 mutations as the cause of an extreme form ofOFD associated with bone dysplasia, tibial defect, cystic kidneys, and brain anomalies (OFD IV, Mohr-Majewski syndrome). Analysis of 184individuals with various ciliopathies (OFD, Meckel, Joubert, and short rib polydactyly syndromes) led us to identify four additional truncating TCTN3 mutations in unrelated fetal cases with overlapping Meckel and OFD IV syndromes and one homozygous missense mutation in a family with Joubert syndrome. By exploring roles of TCTN3 in human ciliary related functions, we found that TCTN3 is necessary for transduction of the sonic hedgehog (SHH) signaling pathway, as revealed by abnormal processing of GLI3 in patient cells. These results are consistent with the suggested role of its murine ortholog, which forms a complex at the ciliary transition zone with TCTN1 and TCTN2, both of which are also implicated in the transduction of SHH signaling. Overall, our data show the involvement of the transition zone protein TCTN3 in the regulation of the key SHH signaling pathway and that its disruption causes a severe form of ciliopathy, combining features of Meckel and OFD IV syndromes.

Ciliogenesis in Caenorhabditis elegans requires genetic interactions between ciliary middle segment localized NPHP-2 (inversin) and transition zone-associated proteins

The cystic kidney diseases nephronophthisis (NPHP), Meckel–Gruber syndrome (MKS) and Joubert syndrome (JBTS) share an underlying etiology of dysfunctional cilia. Patients diagnosed with NPHP type II have mutations in the gene INVS (also known as NPHP2), which encodes inversin, a cilia localizing protein. Here, we show that the C. elegans inversin ortholog, NPHP-2, localizes to the middle segment of sensory cilia and that nphp-2 is partially redundant with nphp-1 and nphp-4 (orthologs of human NPHP1 and NPHP4, respectively) for cilia placement within the head and tail sensilla. nphp-2 also genetically interacts with MKS ciliopathy gene orthologs, including mks-1, mks-3, mks-6, mksr-1 and mksr-2, in a sensilla-dependent manner to control cilia formation and placement. However, nphp-2 is not required for correct localization of the NPHP- and MKS-encoded ciliary transition zone proteins or for intraflagellar transport (IFT). We conclude that INVS/NPHP2 is conserved in C. elegans and that nphp-2 plays an important role in C. elegans cilia by acting as a modifier of the NPHP and MKS pathways to control cilia formation and development.

The ciliary transition zone: from morphology and molecules to medicine

Researchers from various disciplines, including cell and developmental biology, genetics and molecular medicine, have revealed an exceptional diversity of cellular functions that are mediated by cilia-dependent mechanisms. Recent studies have directed our attention to proteins that localize to the ciliary transition zone (TZ), a small evolutionarily conserved subcompartment that is situated between the basal body (BB) and the more distal ciliary axoneme. These reports shed light on the roles of TZ proteins in ciliogenesis, ciliary protein homeostasis and specification of ciliary signaling, and pave the way for understanding their contribution to human ciliopathies. In this review, we describe the interplay of multimeric protein complexes at the TZ, integrating morphological, genetic and proteomic data towards an account of TZ function in ciliary physiology.

Ciliogenesis inCaenorhabditis elegansrequires genetic interactions between ciliary middle segment localized NPHP-2 (inversin) and transition zone-associated proteins

The cystic kidney diseases nephronophthisis (NPHP), Meckel-Gruber syndrome (MKS) and Joubert syndrome (JBTS) share an underlying etiology of dysfunctional cilia. Patients diagnosed with NPHP type II have mutations in the gene INVS (also known as NPHP2), which encodes inversin, a cilia localizing protein. Here, we show that the C. elegans inversin ortholog, NPHP-2, localizes to the middle segment of sensory cilia and that nphp-2 is partially redundant with nphp-1 and nphp-4 (orthologs of human NPHP1 and NPHP4, respectively) for cilia placement within the head and tail sensilla. nphp-2 also genetically interacts with MKS ciliopathy gene orthologs, including mks-1, mks-3, mks-6, mksr-1 and mksr-2, in a sensilla-dependent manner to control cilia formation and placement. However, nphp-2 is not required for correct localization of the NPHP- and MKS-encoded ciliary transition zone proteins or for intraflagellar transport (IFT). We conclude that INVS/NPHP2 is conserved in C. elegans and that nphp-2 plays an important role in C. elegans cilia by acting as a modifier of the NPHP and MKS pathways to control cilia formation and development.

TMEM237 Is Mutated in Individuals with a Joubert Syndrome Related Disorder and Expands the Role of the TMEM Family at the Ciliary Transition Zone

Joubert syndrome related disorders (JSRDs) have broad but variable phenotypic overlap with other ciliopathies. The molecular etiology of this overlap is unclear but probably arises from disrupting common functional module components within primary cilia. To identify additional module elements associated with JSRDs, we performed homozygosity mapping followed by next-generation sequencing (NGS) and uncovered mutations in TMEM237 (previously known as ALS2CR4). We show that loss of the mammalian TMEM237, which localizes to the ciliary transition zone (TZ), results in defective ciliogenesis and deregulation of Wnt signaling. Furthermore, disruption of Danio rerio (zebrafish) tmem237 expression produces gastrulation defects consistent with ciliary dysfunction, and Caenorhabditis elegans jbts-14 genetically interacts with nphp-4, encoding another TZ protein, to control basal body-TZ anchoring to the membrane and ciliogenesis. Both mammalian and C.elegans TMEM237/JBTS-14 require RPGRIP1L/MKS5 for proper TZ localization, and we demonstrate additional functional interactions between C.elegans JBTS-14 and MKS-2/TMEM216, MKSR-1/B9D1, and MKSR-2/B9D2. Collectively, our findings integrate TMEM237/JBTS-14 in a complex interaction network of TZ-associated proteins and reveal a growing contribution of a TZ functional module to the spectrum of ciliopathy phenotypes.

Transition zone proteins and cilia dynamics

New work has identified networks of protein interactions at the transition zones of cilia. These discoveries provide insights into the molecular pathogenesis of ciliopathies and illustrate the power of linking proteomics technologies with human genetics to uncover critical disease pathways.

MKS and NPHP modules cooperate to establish basal body/transition zone membrane associations and ciliary gate function during ciliogenesis

Meckel-Gruber syndrome (MKS), nephronophthisis (NPHP), and related ciliopathies present with overlapping phenotypes and display considerable allelism between at least twelve different genes of largely unexplained function. We demonstrate that the conserved C. elegans B9 domain (MKS-1, MKSR-1, and MKSR-2), MKS-3/TMEM67, MKS-5/RPGRIP1L, MKS-6/CC2D2A, NPHP-1, and NPHP-4 proteins exhibit essential, collective functions at the transition zone (TZ), an underappreciated region at the base of all cilia characterized by Y-shaped assemblages that link axoneme microtubules to surrounding membrane. These TZ proteins functionally interact as members of two distinct modules, which together contribute to an early ciliogenic event. Specifically, MKS/MKSR/NPHP proteins establish basal body/TZ membrane attachments before or coinciding with intraflagellar transport-dependent axoneme extension and subsequently restrict accumulation of nonciliary components within the ciliary compartment. Together, our findings uncover a unified role for eight TZ-localized proteins in basal body anchoring and establishing a ciliary gate during ciliogenesis, and suggest that disrupting ciliary gate function contributes to phenotypic features of the MKS/NPHP disease spectrum.

TheC. eleganshomologs of nephrocystin-1 and nephrocystin-4 are cilia transition zone proteins involved in chemosensory perception

Nephronophthisis (NPH) is a cystic kidney disorder that causes end-stage renal failure in children. Five nephrocystin (nephrocystin-1 to nephrocystin-5) genes, whose function is disrupted in NPH patients, have been identified and data indicate they form a complex at cell junctions and focal adhesions. More recently, the nephrocystin proteins have also been identified in cilia, as have multiple other cystic kidney disease related proteins. Significant insights into this cilia and cystic kidney disease connection have come from analyses in simpler eukaryotic organisms such as Caenorhabditis elegans. In this regard, we became interested in the C. elegans homologs of nephrocystin-1 (nph-1) and nephrocystin-4 (nph-4) from a database screen to identify genes coordinately regulated by the ciliogenic transcription factor DAF-19. Here we show that expression of nph-1 and nph-4 is DAF-19 dependent, that their expression is restricted to ciliated sensory neurons, and that both NPH-1 and NPH-4 concentrate at the transition zones at the base of the cilia, but are not found in the cilium axoneme. In addition, NPH-4 is required for the localization of NPH-1 to this domain. Interestingly, nph-1 or nph-4 mutants have no obvious cilia assembly defects; however, they do have abnormalities in cilia-mediated sensory functions as evidenced by abnormal chemotaxis and lifespan regulation. Our data suggest that rather than having a ciliogenic role, the NPH proteins play an important function as part of the sensory or signaling machinery of this organelle. These findings suggest that the defects in human NPH patients may not be the result of aberrant ciliogenesis but abnormal cilia-sensory functions.