- Research article
- Open Access
Tim50a, a nuclear isoform of the mitochondrial Tim50, interacts with proteins involved in snRNP biogenesis
© Xu et al; licensee BioMed Central Ltd. 2005
Received: 26 January 2005
Accepted: 11 July 2005
Published: 11 July 2005
The Cajal body (CB) is a nuclear suborganelle involved in the biogenesis of small nuclear ribonucleoproteins (snRNPs), which are vital for pre-mRNA splicing. Newly imported Sm-class snRNPs traffic through CBs, where the snRNA component of the snRNP is modified, and then target to other nuclear domains such as speckles and perichromatin fibrils. It is not known how nascent snRNPs localize to the CB and are released from this structure after modification. The marker protein for CBs, coilin, may play a role in snRNP biogenesis given that it can interact with snRNPs and SMN, the protein mutated in Spinal Muscular Atrophy. Loss of coilin function in mice leads to significant viability and fertility problems and altered CB formation.
In this report, we identify a minor isoform of the mitochondrial Tim50, Tim50a, as a coilin interacting protein. The Tim50a transcript can be detected in some cancer cell lines and normal brain tissue. The Tim50a protein differs only from Tim50 in that it contains an additional 103 aa N-terminal to the translation start of Tim50. Importantly, a putative nuclear localization signal is found within these 103 residues. In contrast to Tim50, which localizes to the cytoplasm and mitochondria, Tim50a is strictly nuclear and is enriched in speckles with snRNPs. In addition to coilin, Tim50a interacts with snRNPs and SMN. Competition binding experiments demonstrate that coilin competes with Sm proteins of snRNPs and SMN for binding sites on Tim50a.
Tim50a may play a role in snRNP biogenesis given its cellular localization and protein interaction characteristics. We hypothesize that Tim50a takes part in the release of snRNPs and SMN from the CB.
The biogenesis of most spliceosomal small nuclear ribonucleoproteins (snRNPs) is complicated and requires both cytoplasmic and nuclear maturation steps [1–3]. For example, the spliceosomal small nuclear RNAs (snRNAs) of Ul, U2, U4 and U5 snRNPs are synthesized by RNA polymerase II and may traffic through specific subnuclear domains before being exported to the cytoplasm [1, 3]. In the cytoplasm, a septet of Sm proteins (B/B', Dl, D2, D3, E, F, G) binds the Sm motif of the snRNA under the control of the Survival of Motor Neurons (SMN) protein complex. Mutations in the SMN protein cause the neurodegenerative disorder Spinal Muscular Atrophy [4, 5]. After the Sm core has been assembled onto the snRNA, the snRNA is subject to further processing, followed by import back into the nucleus; again with the help of the SMN complex [1, 5–8].
Upon nuclear re-entry, newly assembled Ul, U2, U4 and U5 snRNPs first localize to a subnuclear domain known as the Cajal body . In the Cajal body (CB), the snRNA component of the snRNP is subjected to pseudouridine-base and 2'-0-methyl sugar-modifications that are guided by small CB-specific RNAs (scaRNAs) [10–12]. These modifications are crucial for proper pre-mRNA splicing in vivo . After their modification in the CB, snRNPs localize to speckles, where they are stored, or perichromatin fibrils, where splicing occurs concurrently with transcription . Unlike Ul, U2, U4 and U5 snRNAs, maturation of the RNA polymerase III-transcribed U6 snRNA does not include a cytoplasmic phase and may take place in the nucleolus and the CB . The U7 snRNP, which is required for histone pre-mRNA 3'-end processing [15–17], is assembled in manner similar to that observed for Ul, U2, U4 and U5 snRNPs, including a cytoplasmic phase . However, U7 snRNA has a noncanonical Sm binding site and thus recruits a different type of Sm core compared to that which binds Ul, U2, U4 and U5 snRNA [19, 20]. Like the spliceosomal snRNPs, the U7 snRNP is enriched within CBs [19, 21]. CBs have been shown to move in an ATP dependent manner [22, 23] as well as associate with various gene loci, including snRNA and histone gene clusters . Consequently, CBs may provide a platform upon which a feedback regulatory mechanism for snRNP and histone biogenesis takes place .
The mechanisms by which snRNPs are targeted to and released from the CB are unknown. One possibility is that a factor within the CB interacts with nascent snRNPs and facilitates their modification. Another factor may displace snRNPs from the CB, allowing for their subsequent localization in speckles and perichromatin fibrils. The CB marker protein coilin may play a role in the targeting of snRNPs to CBs. Removal of coilin in Xenopus by immunodepletion decreases snRNP levels in the amphibian equivalent of the CB . Characterization of coilin knockout mice has revealed that they are viable on an outbred mouse strain, but have significant viability and fertility defects on inbred strains  (Greg Matera, personal communication). Cell lines derived from coilin knockout mice lack canonical CBs in which snRNPs are enriched . However, add-back experiments demonstrate that typical CBs, containing snRNPs, can be reformed upon the addition of coilin . Furthermore, coilin can interact directly with several Sm proteins of snRNPs  (our unpublished observations). Taken together, these data indicate that, while not an essential protein, coilin is important for proper CB formation. Functional CBs may allow for the efficient coordination of the nuclear steps of snRNP biogenesis.
Another protein that requires coilin for its localization to CBs is SMN [27–30]. Coilin directly interacts with SMN via several arginine/glycine (RG) dipeptide repeats in coilin . The arginines within this RG box motif are symmetrically dimethylated [29, 30], resulting in an increased affinity for SMN [31, 32]. In most cell lines and tissues, SMN localizes to the cytoplasm and CBs . However, SMN in some cell lines and fetal tissue localizes to discrete nuclear structures termed "gems" (for Gemini of Cajal bodies) [34, 35]. The presence of gems correlates with a decrease in coilin methylation [29, 30]. Although the nuclear role of SMN is not well understood, it is possible that SMN escorts nascent snRNPs to the CB [6, 8]. Interestingly, coilin can compete with Sm proteins for binding sites on SMN , indicating that locally high concentrations of coilin within the CB may serve to displace snRNPs from the SMN complex. The interplay between SMN, snRNPs and coilin may therefore regulate snRNP accumulation within the CB. We set out to determine if we could identify factors that control the departure of nascent snRNPs from the CB.
In this report, we demonstrate that an isoform of the human mitochondrial Tim50, Tim50a, localizes to speckles and interacts with snRNPs, SMN and coilin. Human Tim50, which has phosphatase activity, is a component of the mitochondrial translocator and regulates mitochondrial integrity and cell death . The protein sequence of Tim50 and Tim50a are identical, with the important exception that Tim50a contains an alternative translational start sequence that adds 103 aa to its N-terminus relative to Tim50. Competition binding experiments show that SmB' does not compete with SMN for Tim50a binding sites, but SmB' does reduce coilin interaction with Tim50a. Furthermore, SMN and coilin compete for Tim50a binding sites and Tim50a forms a more efficient complex with snRNPs in vivo compared to Tim50. Based on these results, we propose that Tim50a is involved in the regulation of snRNP biogenesis and possibly the activity of nuclear SMN.
Results and discussion
Isolation of Tim50a
Given the central role of coilin in the formation and composition of CBs, especially in its ability to recruit the SMN complex and snRNPs, we wanted to identify proteins that interact with coilin and possibly regulate SMN and snRNP localization in the CB. Towards this end, we conducted a yeast two-hybrid screen with coilin as bait. A human brain cDNA library was chosen for this screen because we are interested in assessing CB protein dynamics in neuronal tissue, which is the cell type primarily affected in Spinal Muscular Atrophy. The C-terminal 214 aa of coilin, which interacts with SMN and Sm proteins, was the bait for the screen  (our unpublished observations). Consequently, other proteins that bind C214 may regulate the interplay between coilin/SMN and coilin/Sm and thus play a role in CB dynamics.
To verify the existence of Tim50a in other cell lines and to obtain a general idea as to the abundance of this transcript relative to the Tim50 isoform, we performed nested PCR with primers specific to Tim50a on cDNAs from four additional cancer cell lines: A-549, NIH: OVCAR-3, MDA-MB-231 and HCT-15. Another primer set was used in a standard (not nested) PCR reaction to amplify a region common to both Tim50a and Tim50 (Figure 1B). As shown in Figure 1C (upper panel), a standard PCR reaction (30 cycles) using primers that can bind both Tim50a and Tim50 (ComFor+ComRev) generate a product from all of the cell lines tested. In contrast, standard PCR reactions using Tim50a-specific primers (50aFor+50aRev) fail to yield a product from cell line cDNAs, but successfully generate a product using a positive control plasmid template (our unpublished observations). However, nested PCR (20 cycles) reveals that two of the four cell lines, A-549 and NIH: OVCAR-3, contain the Tim50a transcript (Figure 1C, lower panel), as monitored by sequencing of the product. The lower band in the NIH: OVCAR-3 reaction is from an unrelated transcript. Therefore, while Tim50a mRNA is not nearly as abundant as the Tim50 message, this species is present in at least four different cell lines (two lines from this study and two from the EST database).
Cellular localization of Tim50a
Actinomycin D redistribution of Tim50a
Direct interaction of Tim50a with coilin, SmB' and SMN
SmB' and SMN compete with coilin for Tim50a binding sites
We then tested if coilin and SmB' compete for binding sites on Tim50a. For this experiment, we incubated a fixed amount of GST-Tim50aSac with a constant amount of a coilin fragment (C214) and, in separate reactions, an increasing amount of SmB'. As shown in Figure 7B, increasing the level of SmB' decreases the recovery of the coilin fragment (C214) by GST-Tim50aSac (bottom panel, compare the amount of C214 recovered in lane 4 to that in lane 2). Thus coilin and SmB' compete for binding sites on Tim50a.
Finally we monitored if coilin and SMN compete for the same binding sites on Tim50a. This experiment was conducted with a fixed amount of GST-Tim50aSac and a constant amount of SMN with increasing levels of the coilin fragment (C214). The binding of the respective proteins to the Tim50a substrate in the absence of competitor (Figure 7C) is shown in lane 2 (upper panel) for the coilin fragment and lane 3 (lower panel) for SMN. In reactions with both soluble proteins, as the level of coilin fragment (C214) is increased, the amount of SMN recovered by the Tim50a beads is reduced (compare the SMN signal in lane 7 to that in lane 3). These data are consistent with a competition for Tim50a binding sites by SMN and coilin. Given its protein interaction potential, we hypothesize that Tim50a may affect CB function by interacting with proteins that localize to this domain. One possible scenario is that Tim50a displaces snRNPs from the CB and facilitates their translocation to speckles. Tim50a may also disrupt the interaction between coilin and SMN, allowing for SMN to leave the CB.
Tim50a interacts with SMN and snRNPs in vivo
Given that Tim50a localizes to speckles, in which snRNPs are stored, and directly interacts with a subunit of the Sm core, it is likely that Tim50a will interact with intact snRNPs. However, the in vitro binding data indicate that the mitochondrial isoform, Tim50, also has the potential to interact with snRNPs, which are known to have a cytoplasmic phase. To test this, we conducted a co-immunoprecipitation assay on HeLa cells transfected with empty GFP vector or GFP fused to Tim50a or Tim50. Lysates were generated and subject to incubation with the anti-Sm antibody Y12. After SDS-PAGE and Western transfer, the blot was probed with anti-GFP antibodies to monitor the association of GFP-Tim50a or GFP-Tim50 with snRNPs. As shown in Figure 8B, a signal corresponding to GFP-Tim50a is present in the Y12 immunoprecipitation reaction (lane 5). In contrast, less Tim50 is co-immunoprecipitated by Y12 (lane 6) compared to Tim50a. A GFP-alone signal is not observed in the Y12 reaction (lane 4), demonstrating the specificity of the reaction. Therefore, in vivo, Tim50a appears to be more efficient in snRNP interaction than Tim50, although we have not excluded the possibility that the GFP-tag may adversely affect Tim50 interactions. To address this point, Tim50a and Tim50 proteins were fused to smaller myc-tags, expressed in HeLa cells and tested for interaction with an immobilized Sm protein, SmB'. Both proteins bind GST-SmB', indicating that the GFP-tag may indeed contribute to the reduced interaction of Tim50 with snRNPs (Figure 8C). Alternatively, the faint Tim50 signal observed in the Y12 co-immunoprecipitation reaction (lane 6) may be an artifact due to the overexpression of GFP-Tim50 and subsequent nuclear localization, as shown in Figure 3. In support of this thought, immunofluorescence analysis of endogenous Tim50 demonstrates that this protein is predominantly cytoplasmic with little nuclear accumulation . Given that Tim50a is a nuclear protein, we speculate that Tim50a interactions may regulate the nuclear activity of SMN and trafficking of snRNPs, possibly by altering the dynamics of the association between SMN, coilin and snRNPs. Additionally, it is plausible that cytoplasmic SMN can interact with Tim50 before mitochondrial import.
The cellular localization and protein interaction characteristics of Tim50a suggest that this isoform of Tim50 may play a role in snRNP biogenesis. Based on the abundance of ESTs, it is likely that Tim50, not Tim50a, is the major product of the TIMM50 gene. However, the presence of Tim50a ESTs from cancer cell lines suggests that this protein may be induced in cellular transformation. It is known that cancer cells contain CBs, while some normal cells and tissues do not [41, 35]. For example, normal adult lung tissue does not contain CBs, but lung cancer cells do. Since CBs play a role in snRNP biogenesis, it is likely that the increase of CBs in transformed cells reflects on the heightened demand in splicing requirements for upregulated genes that participate in the establishment and/or maintenance of the altered cellular physiology . The induction of CBs may also facilitate the production of telomerase, the RNA component of which localizes to CBs [43, 44]. In addition to cancer cells neuronal cells contain robust CBs , possibly because high levels of snRNPs are necessary to process the abundance of messages subject to alternative splicing in neuronal tissue . Therefore, Tim50a expression may be limited to tissue with high demands in snRNP metabolism. We are currently developing an antibody to the unique N-terminus of Tim50a in order to explore this possibility. Additionally, experiments are underway to verify the role of Tim50a in snRNP biogenesis. In particular, we are interesting in determining if Tim50a is involved in the liberation of snRNPs from the CB after they have been modified. The functional consequence of the interaction between Tim50a and SMN is also being investigated. Finally we note that Tim50a contains the phosphatase domain shown to be functional in the Tim50 isoform , and thus may alter CB activity by modifying coilin, a known phosphoprotein .
Yeast two-hybrid screen, plasmid construction and mutagenesis
A human brain cDNA library cloned into the prey vector pACT2 and pretransformed into the yeast strain Y187 (BD Biosciences, Palo Alto, CA) was mated with the strain PJ69-2A harboring the bait vector pAS2-l-coilin(362–576, C214) per the manufacturer's instructions. After mating, the yeast were plated onto medium lacking tryptophan, leucine, histidine and adenine (to select for bait, prey and protein interaction). Colonies were picked after several days of incubation and the prey plasmid was isolated and transformed into PJ69-2A containing pAS2-1-C214 or control bait plasmids to confirm the specificity of the interaction. Restriction digests and sequencing revealed that nine different prey cDNAs were recovered, one of which was termed CAP50. CAP50 was sequenced and the results were used to conduct a BLAST search on the NCBI website. Based on this analysis, we concluded that CAP50 contained the partial coding sequence for the protein Tim50 . Several expressed sequence tags (ESTs) corresponding to Tim50 are present in the database. One EST, BE386959, contains upstream sequence information not found in the majority of Tim50 ESTs or reflected in the Tim50 protein sequence. We procured EST BE386959 and used this cDNA as a template in a PCR reaction with primers designed to amplify the Tim50a isoform (Bam HI Forward primer: 5'GTCGGGATCCATGGCCTCAGCTTTATCTCT-3' and Eco Rl reverse primer: 5'-TCGGAATTCGAGGCCCAGAGTTCAGGGCT-3'). The TIM50a amplified product was cloned in frame into the pEGFP-Cl vector (BD Biosciences, Palo Alto, CA) at Eco RI + Bgl II restriction enzyme sites. Tim50a was also cloned in frame into pGEX-2T (Amersham Pharmacia, Uppsala, Sweden) and pET28a (Novagen, Madison, WI) vectors at Eco RI + Bam HI sites and utilized for bacterial protein expression. Various mutants of TIM50a were produced from specific restriction enzyme sites that were located within the TIM50a coding sequence or in pEGFP-C1. These constructs included TIM50aN87 (Sma I deletion), TIM50aSac (Sac I internal deletion) and TIM50aN135 (Apa I deletion). Also, CAP50 obtained from the yeast two-hybrid screen was digested with Bam HI + Bgl II. and cloned in frame into pGEX-2T at a Bam HI site and utilized for bacterial protein expression, or digested with Bam HI + Eco RI and cloned in frame into pEGFP-Cl at the equivalent sites for transient transfection experiments. The mitochondrial Tim50 was cloned into various expression vectors by standard techniques.
PCR and nested PCR of Tim50 isoforms on cancer cell line cDNA
PCR reactions were performed in the DNA Engine PTC-200 Peltier Thermal Cycler (MJ Research, Watertown, MA). The cDNA from four cancer cell lines were kindly provided by Dr. Laree Hiser (The University of Mississippi, Medical Center): NIH: OVCAR-3 (ovarian cancer), HCT-15 (colon cancer), A-549 (non-small cell lung cancer) and MDA-MB-231 (breast cancer). These cDNA were shown by Dr. Hiser to be free of genomic DNA. Two sets of primers were used in the PCR reactions, the sequence of which can be provided upon request. The first set (ComFor+ComRev) was designed to amplify a region common to both Tim50a and Tim50, thus providing a method to monitor the total expression level of the TIMM50 gene. The second set of primers (50aFor+50aRev or 50anRev) bind specifically to Tim50a and not Tim50, thereby allowing the level of the Tim50a transcript to be assessed. A standard reaction, consisting of 30 cycles of amplification and the ComFor + ComRev primers, was used to amplify the common region of Tim50/Tim50a from cDNA. Plasmid containing the Tim50a cDNA (10 ng) and water served as positive and negative controls, respectively. To observe the Tim50a isoform, nested PCR had to be conducted. For these reactions, 30 cycles of amplification using the 50aFor+50aRev primers was conducted using the cDNA as template in a 25 μl reaction. Water and 10 ng of Tim50a plasmid served as negative and positive controls, respectively. 0.1 μl of each product, including the negative and positive controls, was then used as a template in a 25 μl reaction with a second pair of primers (50aFor+50anRev) for 20 cycles of amplification. The resultant products were cloned and sequenced to verify that they were derived from the Tim50a isoform. Nested PCR using NIH:OVCAR-3 cDNA consistently yielded two products. Sequencing demonstrated that the upper product was from Tim50a while the lower product was from an unrelated message with partial homology to the primers used in the nested PCR reaction.
Cell Culture, Transfection, Immunofluorescence, and Immunoprecipitation
HeLa cells from the American Type Culture Collection (ATCC) were cultured, transfected with Superfect (Qiagen, Valencia, CA) and processed as described [28, 29, 47]. Where indicated, actinomycin D was used at 5 μg/ml for two hours. For immunofluorescence, cells were grown on chamberslides and fixed with 4% paraformaldehyde followed by the permeabilization with 0.5% Triton X-100. The permeable cells were then blocked with 10% normal goat serum for 30 min and probed with the corresponding primary and secondary antibodies. For immunoprecipitation, whole cell lysate was obtained from HeLa cells transfected with specific constructs. Cells were lysed in 50 mM Tris, pH 7.5, 150 mM NaCl, 1% NP-40,1% sodium deoxycholate, 0.1% SDS, 2 mM EDTA plus 1 tablet of complete protease inhibitor cocktail (Roche, Mannheim, Germany) per 50 ml lysis solution. The lysates were then repeatedly passed through a 25-gauge needle to shear DNA. The cell lysate was incubated at 4°C for one hour with primary antibody, followed by the addition of Sepharose beads (Amersham Pharmacia, Uppsala, Sweden) and an additional one hour of incubation. Both incubation periods were accompanied with gentle rotation. The beads were washed with 1 ml lysis solution 5 times, resuspended in 5X SDS loading buffer, boiled, and subject to SDS-PAGE and Western blotting as described . Antibodies used for this experimentation include anti-SMN (BD Biosciences, Palo Alto, CA, catalog number 610646), anti-GFP (polyclonal, BD Biosciences, Palo Alto, CA, catalog number 632459; monoclonal, Roche, Indianapolis, IN, catalog number 1814460) and anti-Sm (Y12) (Lab Vision, Freemont, CA, catalog number MS-450-P).
In vitro binding assays
GST-tagged and His-tagged constructs, after transformation into E. coil BL21(DE3)pLysS cells, were induced and purified as described . In binding reactions, approximately 1 μg of His-T7-tagged protein was incubated with 1 μg of the GST-fusion protein in 1 ml of lysis buffer plus 2 mM DTT. After incubation for 1 hour at 4°C with gentle inversion, the beads were washed 5 times (1 ml each) with lysis buffer plus DTT, resuspended in 10 μl 5X SDS loading buffer, boiled and subjected to SDS-PAGE. Primary antibodies used included anti-T7 (Novagen, Madison, WI, 1:1000), anti-SMN (described above) and anti-coilin , 1:500). Competition experiments were performed as described , except that increasing amounts of SmB' or coilin fragment were used.
We thank Kecia Grant for her excellent technical assistance and Dr. Greg Matera (Case Western Reserve University, Cleveland, OH) for the anti-coilin antibodies. We also thank Dr. Laree Hiser (The University of Mississippi, Medical Center) for the cancer cell line cDNAs and Drs. Archa Fox and Angus Lamond (University of Dundee, Scotland) for their kind gift of anti-PSPl antibodies. This work was supported by a grant from the Muscular Dystrophy Association.
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