Novel interactions of CLN5 support molecular networking between Neuronal Ceroid Lipofuscinosis proteins
- Annina Lyly†1,
- Carina von Schantz†1,
- Claudia Heine1,
- Mia-Lisa Schmiedt1,
- Tessa Sipilä1,
- Anu Jalanko1 and
- Aija Kyttälä1Email author
© Lyly et al; licensee BioMed Central Ltd. 2009
Received: 11 June 2009
Accepted: 26 November 2009
Published: 26 November 2009
Neuronal ceroid lipofuscinoses (NCLs) comprise at least eight genetically characterized neurodegenerative disorders of childhood. Despite of genetic heterogeneity, the high similarity of clinical symptoms and pathology of different NCL disorders suggest cooperation between different NCL proteins and common mechanisms of pathogenesis. Here, we have studied molecular interactions between NCL proteins, concentrating specifically on the interactions of CLN5, the protein underlying the Finnish variant late infantile form of NCL (vLINCLFin).
We found that CLN5 interacts with several other NCL proteins namely, CLN1/PPT1, CLN2/TPP1, CLN3, CLN6 and CLN8. Furthermore, analysis of the intracellular targeting of CLN5 together with the interacting NCL proteins revealed that over-expression of PPT1 can facilitate the lysosomal transport of mutated CLN5FinMajor, normally residing in the ER and in the Golgi complex. The significance of the novel interaction between CLN5 and PPT1 was further supported by the finding that CLN5 was also able to bind the F1-ATPase, earlier shown to interact with PPT1.
We have described novel interactions between CLN5 and several NCL proteins, suggesting a modifying role for these proteins in the pathogenesis of individual NCL disorders. Among these novel interactions, binding of CLN5 to CLN1/PPT1 is suggested to be the most significant one, since over-expression of PPT1 was shown to influence on the intracellular trafficking of mutated CLN5, and they were shown to share a binding partner outside the NCL protein spectrum.
Neuronal ceroid lipofuscinoses (NCLs) are the most common group of children's progressive neurodegenerative disorders with an estimated incidence of 1:12500 in the USA and Nordic countries and approximately 1:100 000 worldwide [reviewed in [1, 2]]. NCL disorders are mostly recessively inherited, and to date, eight different genes have been characterized to underlie these diseases [3–5]. Despite having genetic heterogeneity, NCL diseases resemble each other both clinically and neuropathologically. The clinical course varies from severe congenital disease to milder adult-onset forms. NCLs are phenotypically expressed by progressive mental deterioration, blindness, epileptic seizures and premature death. The pathological findings of these lysosomal storage disorders include intracellular accumulation of autofluorescent lipopigment with variable ultrastructural appearance as well as progressive loss of neocortical neurons. The major component of the intracellular storage material is either the subunit c of the mitochondrial ATP synthase  or sphingolipid activator proteins A and D [5, 7]. More recent analyses of different mouse models of NCL have exposed additional common features in the brain pathology [reviewed in ].
The proteins encoded by NCL genes are localized in different compartments of the secretory pathway. Palmitoyl protein thioesterase 1 (PPT1; CLN1), tripeptidyl-peptidase 1 (TPP1; CLN2) and cathepsin D (CLN10) are soluble lysosomal enzymes [9–11]. CLN3 and the recently identified MFSD8 (CLN7) are transmembrane proteins localizing mainly to the late endosomal/lysosomal compartments [4, 12]. Two of the NCL proteins, CLN6 and CLN8, reside mainly in the ER [13, 14]. Despite the fact that many NCL proteins were characterized already a decade ago, the physiological functions of most NCL proteins are still not known and neither are the molecular connections between them understood . CLN5 is a glycoprotein disrupted in the Finnish variant late infantile form of NCL (vLINCLFin) [16, 17]. The subcellular localization of overexpressed CLN5 has been studied in BHK-21, HeLa and COS-1 and cells, where it was found to be lysosomal [16, 18]. In neuronal cells, CLN5 is also present in the cellular extensions, but the specific organelle localization in neurons is still unidentified . PPT1/CLN1 and CLN3 are also found in neuronal axons, where CLN1 has been localized to synaptic vesicles and CLN3 to synaptosomes [19–21]. Controversial data has been reported about the solubility of the CLN5 protein [16, 18, 22, 23], but both human and mouse CLN5 have been found in the mannose 6-phosphoproteome, supporting the presence of soluble CLN5 variants [24, 25]. Overall, the CLN5 protein is not well conserved, lacks protein homologues and is currently poorly characterized. Very little is also known about the interactions between different NCL proteins. Vesa and co-workers have shown by co-immunoprecipitation and in vitro binding assays that CLN5 interacts with both CLN2 and CLN3 , but the result has not been verified.
To obtain more knowledge of common pathways in NCLs, we examined the interactions of CLN5 with other NCL proteins utilizing pull-down and co-immunoprecipitation analyses. We report four novel interactions for CLN5 and show that PPT1/CLN1 and CLN5 are connected at the level of intracellular trafficking.
Recombinant CLN5-cDNA constructs
Mouse Cln5-cDNA lacking the suggested signal sequence (aa 26-341) was cloned in frame with an N-terminal GST-tag in a pGEX2T vector (Amersham Biosciences). For the co-immunoprecipitation assay, the full-length mCln5-cDNA (aa 1-341) was cloned into the pcDNA3.1A/Myc-His expression vector (Invitrogen) to produce a CLN5 protein with a C-terminal tag. The trafficking-deficient human CLN5-TD (CLN5 flag330) protein was obtained by inserting an intramolecular flag sequence after amino acid 330 into the full-length CLN5 (aa 1-407) pCMV5 construct, using the QuickChange Site-Directed mutagenesis kit. All constructs were verified by sequencing.
Cell culture, transfection and immunofluorescence analyses
HeLa and COS-1 cells were cultured in Dulbecco's modified Eagle's medium (DMEM), supplemented with 10% fetal calf serum (FCS) and 1% antibiotics (penicillin/streptomycin). For transient transfections, cells were plated on 6-well plates and the transfection was performed with Lipofectamine™ 2000 (Gibco Life Technologies) or Fugene HD (Roche Diagnostics) transfection reagents according to manufacturers' instructions. For immunofluorescence analysis, transiently transfected cells were grown on coverslips, fixed with ice-cold methanol 48 h after transfection and stained with the specific antibodies described below. The labeled coverslips were mounted using GelMount (Biomeda Corp., Foster City, CA) and visualized using Leica DMR confocal microscope with TCS NT software (Leica Microscope and Scientific Instruments Group). Adobe Photoshop and Adobe Illustrator softwares were used for image processing. All transfection and immunofluorescence experiments were repeated at least three times.
The human CLN5 protein was detected either with a polyclonal rabbit antibody (1RmI-4) raised against GST-mCLN5 (aa 40-284) or with a guinea pig antibody (1GmII-3) raised against GST-mCLN5 (aa 40-341) . PPT1 and CLN2 were detected with anti-PPT1 antibodies (WB: rabbit polyclonal antibody 8414, 1:500 ; IF: rabbit polyclonal antibody AA-PPT1, 1:200  and mouse anti-CLN2 antibody 8C4, 1:20  kindly provided by Drs. Kida and Golabek (New York, USA). CLN3 was detected with the peptide antibody 385 . CLN8 was detected with a rabbit peptide antibody 391 (1:200)  and mouse monoclonal anti-HA antibody (Boehringer Mannheim). The mouse monoclonal anti-LAMP-1 antibody H4A3 (WB, IF 1:200) was obtained from the Developmental Studies Hybridoma Bank (University of Iowa, Iowa City). The mouse monoclonal anti-FLAG antibody was from Sigma and the mouse anti c-myc antibody (9E10) and the anti-his antibody from Santa Cruz Biotechnology. The mouse monoclonal PDI (Protein Disulfide Isomerase) antibody was obtained from Stressgen. The α- and β-subunits of the mitochondrial ATP synthase were detected with monoclonal antibodies from Molecular Probes. The secondary antibodies used for the immunofluorescence analyses were from Jackson ImmunoResearch and HRP-conjugated antibodies used for Western blot detection were from DAKO.
Cln1-/- (Ppt1Δex4) mice  and Cln5-/- mice  used in this study were maintained on a congenic C57/BL6J strain background. The study has been carried out following good practice in laboratory animal handling and the regulations for handling genetically modified organisms, and it was approved by the Laboratory Animal Care and Use Committee of the National Public Health Institute, Helsinki. Tissues for liver extraction were from adult mice.
Quantitative Real-time PCR
Real-time PCR was performed as described in . In short, Cln5-/-, Cln1-/- and wild-type cortices were prepared and total RNA was extracted using RNeasy Mini kit (Qiagen) according to the manufacturer's instructions, followed by quantification by spectrophotometry. To average out the inter-individual variability, RNA was extracted from the whole cortical area of four Cln5-/- mice, four Cln1-/- mice and four of their respective wt littermates and pooled together into two wild-type and two knock-out samples. To eliminate genomic DNA, RNA was treated with DNAse I (Roche, Mannheim, Germany). The RT reactions were carried out on 300 ng of RNA using TaqMan Reverse transcription kit with Random hexamer primers (Applied Biosystems, Foster City, CA) as recommended by the manufacturer. TaqMan Gene Expression Assays of selected genes were purchased from Applied Bio systems (CLN5 Mm00515002_m1, PPT1 Mm00727515_s1). The mRNA expression levels of these genes and a standard house-keeping gene, mouse TATA-box binding protein (Tbp, Mm 00446973_m1), were quantified using real-time PCR analysis (TaqMan chemistry) on an ABI prism 7700 sequence detection system (PE Applied Bioscience, Warrington, UK). The PCR reactions (25 μl) were carried out in triplicate with TaqMan Universal Master Mix according to the manufacturer's instructions using the following parameters: 50°C for 2 min, 95°C for 10 min, 50 cycles of 95°C for 15 sec, 60°C for 60 min. Relative levels of the selected genes were calculated using the ΔΔCT method  as described previously . The absolute change in expression level is given by 2-ΔΔCT. For illustrative purposes, the value for the wt gene expression was set to 1 and CLN5 as well as PPT1 expression values are shown relative to that.
GST pull-down assays
The GST-mCLN5 fusion construct was expressed in E. coli and purified by binding to the glutathione-Sepharose 4B beads (Amersham Biosciences) for 2 h at 4°C. For the search of NCL binding partners, cytosolic extracts of COS-1 cells were prepared by lysing the cells in lysis buffer (25 mM HEPES pH 7.4, 150 mM NaCl, 1 mM EDTA, 0.5% Triton X-100, 0.5 mM MgCl2 and protease inhibitors) and removing the cell debris by centrifugation. GST vector control and GST-mCLN5 fusion protein were incubated with 4 ml of COS lysates (~2 mg/ml) overnight at 4°C. The beads were washed five times with lysis buffer and the samples were separated by SDS-PAGE under reducing conditions, immunoblotted and probed for different NCL proteins.
The α- and β-subunits of the mitochondrial ATP synthase were pulled down with GST-mCLN5 and GST-hPPT128-306  from the enriched lysosomal/mitochondrial fraction originating from the mouse liver. Briefly, mouse liver of wt, Cln5-/- or Cln1-/- mouse was homogenized (1 g of liver in 5 ml of HB) in HB buffer (320 mM saccharose, 4 mM HEPES pH 7.4, 1 mM MgCl2, 0.5 mM CaCl2 + protease inhibitors) and centrifuged at 3500 rpm for 10 min at 4°C. The post-nuclear supernatant was transferred to clean tubes and centrifuged again at 14 000 rpm for 15 min at 4°C. The pellet was then dissolved with 1.5 ml of EB buffer (100 mM NaCl, 50 mM HEPES pH 7.4, 5 mM MgCl2, 0.5% Triton X-100 + protease inhibitors). The GST pull-downs were done by incubating 1 ml (2.5 mg/ml) of enriched liver lysosomal/mitochondrial fractions with different GST fusion proteins (GST, GST-mCLN5, GST-hPPT1) over night at 4°C. The beads were then carefully washed with the EB buffer. Samples were separated by SDS-PAGE, immunoblotted and probed for α- and β-subunits. All pull-down experiments were repeated at least twice.
PPT1/CLN1 was transiently expressed together with mCLN5-myc/his or with an OPR1L-his  control protein in COS-1 cells. The cells were lysed into an immunoprecipitation buffer (IP buffer: 10 mM Hepes pH 7.4, 150 mM NaCl, 0.5 mM MgCl2, 10% glycerol, 0.5% Triton X-100, + protein inhibitor cocktail) and the cell debris was removed by centrifugation. Immunoprecipitation was done by adding a his-specific antibody (1 μg/ml) and incubating the samples on ice for three hours. Immunocomplexes were then captured by incubation with Protein A/G Plus agarose beads (Santa Cruz) over night at 4°C. Agarose beads were then gently centrifuged (3000 rpm for 30 sec.) and washed three times with the IP-buffer. Samples were separated by SDS-PAGE, immunoblotted and probed for PPT1/CLN1.
Interactions of CLN5 with other NCL proteins
Analyses of intracellular trafficking of CLN5 together with the interacting proteins
To dissect the role of CLN5 interactions with other NCL proteins in vivo, we first compared the localization of the newly characterized interaction partners in wild type and Cln5-/- mouse fibroblasts . Fibroblasts were transiently transfected with constructs producing different NCL proteins (CLN1, 3, 6 and 8, whereas CLN2 could be detected endogenously) and fluorescently labeled with antibodies against the NCL proteins as well as specific organelle markers. However, no differences in the localization of any of the interacting NCL proteins could be detected between the wild type and Cln5-/- cells (data not shown). We also studied the possible effects of simultaneous overexpression of wild type hCLN5 and the interaction partners on the protein localization in HeLa cells. Transient overexpression did not influence the localization of CLN1, CLN2, CLN6 or CLN8 (data not shown). The hydrophobic CLN3 was found in lysosomes, but was often detected also in the ER together with CLN5, most probably reflecting a folding defect in a situation in which two proteins are overexpressed (data not shown). This could reflect an overloading of the ER protein folding machinery.
Overexpression of wild type PPT1/CLN1 rescues the lysosomal trafficking of CLN5FinMajor polypeptide
PPT1/CLN1 mutants retained in the ER do not restrict the lysosomal trafficking of CLN5
Co-immunoprecipitation and compensatory mRNA expression support the relationship between CLN1 and CLN5
Real time PCR was performed from the cortices of wt, Cln1 and Cln5 deficient mice to detect the possible dependence of the disruption of one binding partner on the expression of the other. Analyses of mRNA expression levels in brain tissues showed significant upregulation of the Cln1 mRNA in the four-month old Cln5 deficient mice, indicating a possible compensatory response. The mRNA levels of Cln5 were only slightly upregulated in the brain tissue of the Cln1 deficient mice (Fig. 6B). Altogether, these results strengthened our novel findings and suggested a possible functional connection between CLN1 and CLN5 proteins.
Interaction of CLN5 with the subunits of F1-ATP synthase
Clinical and neuropathological similarities in NCL disorders may result from functional redundancy or co-operation of different NCL proteins. Initial evidence of co-operation has previously been obtained from activity measurements and gene expression analyses. For example, CLN2/TPP1 activity has been shown to be elevated in other forms of NCL [23, 36, 37]. Furthermore, the mRNA expression levels of a variety of NCL genes have been reported to be altered in different NCLs . Recent studies of animal models have further supported a common mechanism in the disease pathogenesis of the NCLs. Selective loss of interneurons, early defects on thalamocortical neuron survival as well as early glial responses are detected in different mouse models as well as in large animal models [8, 38]. Molecular interactions between NCL proteins have also been reported previously [23, 39]. Here we continued the search for NCL protein interactions and their intracellular consequences. We demonstrate that CLN5 has molecular connections to at least to five other NCL proteins, namely CLN1/PPT1, CLN2/TPP1, CLN3, CLN6 and CLN8, suggesting a central role for CLN5 in the NCL network.
Mutations of CLN5 and consequent trafficking defects can result in functional consequences on the interacting proteins, as well as in changes in their distribution. Most NCL proteins are not, however, detectable endogenously by immunofluorescence analyses using the currently available antibodies and therefore this hypothesis could not be tested in patient fibroblasts. However, simultaneous overexpression of binding partners with the modified, transport incompetent CLN5-TD (CLN5-flag330) construct suggested that the interaction between PPT1/CLN1 and CLN5 is strong and occurs already in the ER, where the interactions between CLN5 and the two ER resident NCL proteins, CLN6 and CLN8, would also naturally occur. Since CLN5 resides in the lumen of intracellular organelles, interaction between CLN5 and the transmembrane proteins must be mediated by the lumenal domains of these proteins. The finding that NCL interactions can occur already in the ER is important since previous studies have also suggested that the ER is an important organelle for the function and/or trafficking of NCL proteins. For example, CLN3 carrying the most common JNCL mutation  has been reported to preserve a significant function in the ER. Although the mutated CLN3 is retained in the ER, it was shown to be able to affect the size of lysosomes . Furthermore, our data suggest that TPP1/CLN2, another lysosomal enzyme, is likely to interact with CLN5 only in the late endosomes/lysosomes. This was supported both by the interaction analysis and the unaffected transport of CLN2. Therefore, the present data suggest that interactions between CLN5 and other NCL proteins can occur along the secretory pathway, and the interactions are not strictly dependent on the steady-state localization or the solubility of the NCL proteins.
Based on our trafficking experiments, the main focus was on the interaction between PPT1/CLN1 and CLN5. Unlike the transport deficient, strictly ER-resident CLN5-TD, the ER exit competent CLN5FinMajor did not prevent the lysosomal trafficking of PPT1 but rather, PPT1 was able to facilitate the trafficking of the mutated CLN5 from the ER and Golgi to the lysosomes. Lysosomal proteins have also previously been shown to assist each other in their lysosomal trafficking. For example, the CLC7 chloride transporter, involved in an NCL-like disorder in mouse, has been shown to facilitate the transport of Ostm1 to the lysosomes, where the proteins act together in lysosomal chloride transport . It was also recently demonstrated that the lysosomal membrane protein LIMP-2 is required for the mannose 6-phosphate receptor-independent targeting of β-glucocerebrosidase. Interestingly, the overexpression of LIMP-2 was also able to facilitate the transport of the mutated, trafficking deficient β-glucocerebrosidase from the ER to the lysosomes . Both PPT1 and CLN5 are soluble intravesicular proteins and are not able to interact with cytoplasmic sorting and transport machinery per se, like CLC7 and LIMP-2. However, trafficking of CLN1/PPT1 has been reported to show properties different from classic lysosomal enzymes  and we have recently discovered that also CLN5 can use M6PR-independent pathways for its lysosomal trafficking (our unpublished observations). Therefore, it is possible that the formation of the CLN1-CLN5 complex may be important for utilizing other trafficking pathways than the classical M6PR pathway. In which circumstances this is required in vivo, remains to be studied in further experiments.
A close connection between PPT1/CLN1 and CLN5 has already been suggested in previous studies. The proteins share similar expression patterns in the mouse brain and in the prenatal human brain [16, 21, 44, 45]. Our recent global gene expression profiling analyses of the Cln1-/- and Cln5-/- mouse brains implicated a common defective pathway mediated by phosphorylation and potentially affecting the maturation of axons and neuronal growth cones . Here, we provide further evidence for a tight relationship between the two proteins by showing not only the interaction between the proteins but also, demonstrating significantly increased expression levels of Cln1 mRNA in the Cln5-/- mouse brain tissue. This suggests a possible compensatory role for PPT1 in CLN5 deficiency. Functional connection of CLN5 and PPT1 is also suggested by the shared interaction partner not belonging to the NCL protein family, the F1-ATP synthase. The ectopic F1-ATP synthase has been shown to function as an apoA-I receptor on the plasma membrane  and both the amount of the F1-complex as well as the uptake of apoA-I have been shown to be increased in Cln1-/- mouse neurons . Therefore, both PPT1 and CLN5 could be connected to the maintenance of lipid homeostasis. In general, accumulating evidence has indicated dysregulated lipid metabolism in different forms of NCLs and several NCL proteins have been functionally linked to lipid metabolism [[48, 49], reviewed in [50–52]].
In this study, we show novel interactions between the neuronal ceroid lipofuscinosis protein CLN5 and five other NCL proteins. Consequently, our study strengthens the long-term hypothesis of a common cellular pathway behind the NCLs and suggests that different mutations in a given NCL protein may lead to different pathological outcomes through variable distinct effects on the NCL protein network. The strongest interaction was detected between CLN5 and PPT1/CLN1, and PPT1/CLN1 was shown to be able to contribute to the intracellular trafficking of the mutated CLN5, the phenomenon, which may be important when planning the therapy for vLINCLFin. Deficiency of Cln5 was also shown to result in upregulation of Cln1 expression in the mouse brain, suggesting a dependency for CLN1/PPT1 over CLN5. For the first time, the two NCL proteins were shown to share an interaction partner outside the NCL protein spectrum, since CLN5 and PPT1 both interacted with the F1-complex of the ATP synthase. This finding may be important in characterization of the cellular functions of the NCL proteins.
The authors wish to express their gratitude to Auli Toivola and Kaija Antila for superb technical assistance. Riitta Paakkanen is thanked for the help in the immunofluorescence studies. Robert M. Badeau is acknowledged for revising the language of the manuscript. This study has been supported by the European Commission (LSHM-CT-2003-503051 to AJ); Academy of Finland (213506 to AJ); Arvo and Lea Ylppö Foundation (to AL), Rinnekoti Foundation (to AL); Sigrid Juselius Foundation (to AJ); The Finnish Cultural Foundation (to CvS).
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