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The Journal of Immunology, 1998, 160: 936-942.
Copyright © 1998 by The American Association of Immunologists

Translational Efficiency Is Up-Regulated by Alternative Exon in Murine IL-15 mRNA1

Hitoshi Nishimura2, Junji Washizu, Nobuhisa Nakamura, Atsushi Enomoto and Yasunobu Yoshikai

Laboratory of Host Defense and Germfree Life, Research Institute for Disease Mechanism and Control, Nagoya University School of Medicine, Nagoya, Japan


    Abstract
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
IL-15 promotes the growth of T cells and shares properties of IL-2. IL-2 is produced exclusively by T cells, while IL-15 message is expressed by a variety of tissues. However, it has been difficult to demonstrate IL-15 in the supernatants of many cells that express message for this cytokine. This suggests that IL-15 production is regulated by post-transcriptional controls. In this study, we cloned three types of murine IL-15 cDNA isoforms generated by alternative splicing and compared the translational efficiency among these isoforms. The translational efficiency of isoforms with alternative exon 5 containing another 3' splice site was significantly higher than that of IL-15 cDNA with originally described exon 5, which is generated by internal splicing of alternative exon 5. The translation product of the isoform containing alternative exon 5 has a shorter open reading frame due to stop codons in additional sequence, followed by a new AUG codon, and displays a shorter leader sequence. The shorter isoform of the IL-15 was detected in peritoneal macrophages stimulated with IFN-{gamma} and LPS, which expressed an abundant level of alternative exon 5. These results suggest that normal IL-15 production in stimulated macrophages is regulated by splicing of alternative exon 5.


    Introduction
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
IL-15 is a novel growth factor for activated {alpha}ß T, {gamma}{delta} T, B, and NK cells that use ß- and {gamma}-chains of IL-2R for signal transduction and shares many properties with IL-2 (1, 2, 3, 4, 5, 6). Although IL-15 belongs to the four-helix bundle cytokine family, the primary structure of IL-15 has no significant homology with IL-2 (1, 7). Analysis of the genomic structure of IL-15 revealed that the IL-15 locus contains eight exons and seven introns, which differs from the four exon/three intron structure of several cytokine genes including that of IL-2 (1, 7). The putative amino acid sequences from full length IL-15 cDNA revealed that it encodes a 162-amino acid precursor peptide with an extremely long 48-amino acid leader peptide in both humans and mice (1, 7). IL-2 is produced mainly by T cells, while IL-15 mRNA is expressed most abundantly in placenta, skeletal muscle, kidney, and LPS-stimulated monocytes/macrophages (1). We and others showed that the expression levels of IL-15 mRNA are increased in macrophage/monocytes by stimulation with IFN-{gamma} and LPS, infection of Salmonella choleraesuis, Mycobacteria tuberculosis, Toxoplasma gondii, or Herpes virus-6 (4, 5, 8, 9). It thus appears that IL-15 has some functions other than those shared with IL-2, such as a role in the cellular response of defense against invading pathogens. However, it has been difficult to demonstrate IL-15 in the supernatants of various cells/tissues that express message for this cytokine. Secretion of biologically active IL-15 has been detected in a few cell lines such as CV-1-EBNA, from which the simian IL-15 gene was originally cloned, and HTLV-I3-infected cell line HuT-102 (1, 2). IL-15 synthesis by HuT-102 involves a marked increase in IL-15 mRNA translation, secondary to the putative proximal integration of the HTLV-I provirus with the proviral fragment and the consequent production of a fusion HTLV-IR/IL-15 mRNA that lacks many upstream AUGs (10). This suggests that normal IL-15 production is regulated at the protein level by post-transcriptional control in addition to the controls of transcription and message stabilization.

In this study, to understand the regulatory mechanism of IL-15 production, we cloned three types of murine IL-15 cDNA generated by alternative splicing and compared the efficiency of translation among these mRNA. Sequence analysis of the cloned cDNA revealed mRNA containing all exons, exon 2-deleted isoform, or exon 2-deleted isoform containing an additional sequence, which we termed {phi}, between exons 4 and 5. The genomic sequence between exons 4 and 5 revealed that the new sequence matched exactly the sequence located just upstream originally defined exon 5. This suggests that the IL-15 mRNA isoform with alternative exon 5 is generated by alternative splicing at a different splice site upstream of exon 5. Although there was no difference in the level of transcription among the three splicing products as assessed by Northern hybridization, the translation efficiency of isoform containing alternative exon 5 with the novel sequence was significantly higher than those of the IL-15 cDNA with exon 5. The translation product of the isoform containing an alternative exon 5 has a shorter open reading frame (ORF) due to stop codons in the novel sequence, followed by a new AUG codon, and displays a shorter leader sequence but shares the same amino acid composition as mature IL-15 protein. The shorter isoform of IL-15 precursor was detected in peritoneal macrophages stimulated with IFN-{gamma}/LPS, which expressed an abundant level of an alternative exon 5. The implications of these findings concerning post-transcriptional control of IL-15 production are discussed.


    Materials and Methods
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Cells

The monocyte/macrophage cell lines J774A.1 derived from BALB/c mice, provided by the American Type Culture Collection (Bethesda, MD), were cultured in RPMI 1640 medium, supplemented with L-glutamine (4 mM) and 10% heat-inactivated FCS. The cells were subcultured twice weekly. Peritoneal macrophages were prepared as described (11). Briefly, peritoneal exuded cells were plated and allowed to adhere for 2 h at 37°C. More than 95% of adherent cells were macrophages as assessed by morphologic characteristics, esterase staining using {alpha}-naphtylacetate (Sigma, St. Louis, MO), and latex ingestion (1.1 µm diameter) (Dow Chemical, Indianapolis, IN).

Antibodies

Neutralizing mAb (rat IgG1, G277-3588) to the murine IL-15 was purchased from PharMingen (San Diego, CA). Neutralizing anti-IL-2 mAb (rat IgG2ak, (No. 40014) and anti-IL-4 mAb (rat IgG1k, No. 40034) were purchased from Becton Dickinson (Bedford, MA). Isotype control Abs (rat IgG) were purchased from Inter-Cell Technologies (Hopewell, NJ).

RT-PCR

mRNA was extracted from the stimulated-macrophages using a QuickPrep Micro mRNA Purification Kit (Pharmacia Biotech, Uppsala, Sweden). First-strand cDNA synthesis and RT-PCR proceeded as described by Saiki et al. (12). First-strand cDNA was synthesized from 2 µg of mRNA using reverse transcriptase SuperScriptTM II RT (Life Technologies, Gaithersburg, MD) and 20 pmol of random primer (Life Technologies) in 20 µl of reaction mixture, according to the manufacturer’s instructions. The synthesized first strand of cDNA (2 µl) was amplified by means of the PCR using 40 pmol of each primer with 2.5 U of recombinant Taq (Takara Shuzou, Osaka, Japan) in a total volume of 100 µl of reaction buffer consisting of 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM MgCl2, 0.01% gelatin, and 0.2 µM dNTP, as well as 20 pmol of specific primers for IL-15 exons (7) and ß-actin as follows: exon 1 sense, GCTGTGTTTGGAAGGCTGAGTT (position 203–224 in murine IL-15 cDNA sequence); exon 3 sense, AGCTCTTACCTGGGCATTAA (position 443–462); exon 4 sense, TCCATCTCGTGCTACTTGTGTTTCC (position 499–523); antisense, AACACAAGTAGCACGAGATGGA (position 499–520); exon 6 and 7 sense, GTGACTTTCATCCCAGTTGC (position 695–714); exon 8 sense, CGTGCTCATGGCTGGTGCAAAG (position 856–875); antisense, ATGGAGCTGTGCTGCCTCT (position 1010–1028); additional sequence {phi} antisense, AAGCAACGGAACAATCAAGA (position 56–75 in additional sequence {phi}); ß-actin sense, TGGAATCCTGTGGCATCCATGAAAC; antisense, TAAAACGCAGCTCAGTAACAGTCCG.

PCR thermocycles consisted of 1 min at 94°C, followed by 1 min at 54°C, and 30 s at 72°C. Before the first cycle, a denaturation step for 7 min at 94°C was included, and after 28 cycles the extension was prolonged for 4 min at 72°C. The PCR product was resolved by electrophoresis on a 1.8% agarose gel (Nakalai Tesque, Kyoto, Japan) and transferred to a GeneScreen plus filter (NEN Research Products, Boston, MA), then hybridized with a 32P-labeled oligo probe as follows: IL-15 exon 7 (5'-GCAATGAACTGCTTTCTCCTG-3', position 724–744 in murine cDNA sequence) (7). After the membranes were incubated for 16 h at 60°C in 1 M NaCl, 10% dextran sulfate, and 100 µg/ml heat-denatured salmon sperm DNA, they were washed for 30 min in 2x SSC and 1% SDS at 60°C and exposed to a phosphor imaging plate for visualization on a Fuji BAS-2000 phosphor imaging system (Fuji Photo Film Co., Tokyo, Japan). Raw data of radioactivity are presented as photo-stimulated luminescence value (PSL)/area (mm2) according to manufacturer’s instruction.

Cloning of IL-15 cDNA and nucleotide sequencing

RT-PCR products were resolved in low-melting agarose gels, isolated, and cloned into TA vector PCR II (Invitrogen, San Diego, CA). Purified dsDNAs were sequenced using the Taq Dye Primer Cycle Sequencing Kit and an ABI 373A DNA sequencer (Applied Biosystems, Foster City, CA).

Cloning of intron between exons 4 and 5 of murine IL-15 gene

Introns between exons 4 and 5 of murine IL-15 gene were cloned by PCR of genomic DNA using specific primer for exon 5 and Promoter Finder DNA Walking Kits (Clontech Laboratories, Palo Alto, CA). Genomic DNA from DraI library in the kit was amplified by two rounds of PCR. The sense primers provided in the kit were used. The antisense primer for first-round PCR was exon 5-1 (5'-TAAGGCTTTCAATTTTCTCCAGGTC-3', position 631–655 in murine IL-15 cDNA sequence), and the antisense primer for second-round PCR was exon 5-2 (5'-TCTTACATCTATCCAGTTGGCCTCT-3', position 603–627) (7). The PCR products approximately 2 kbp were subcloned into TA vector PCR II (Invitrogen) and subjected to sequence analysis.

In vitro transcription/translation assay

IL-15 cDNA was cloned into PCR III vectors (Invitrogen) containing a T7 promoter site and a bovine growth hormone polyadenylation signal. We used the TNT T7 (transcription and translation)-coupled reticulocyte lysate system (Promega, Madison, WI) and a cloned IL-15 PCR III vector (1 µg). We followed recommendations of Promega for [35S]methionine labeling. We examined the transcriptional level in the reticulocyte lysate by Northern hybridization using an IL-15 cDNA probe. Briefly, total RNA was extracted from the programmed lysates with acid guanidinium thiocyanate-phenol-chloroform (13). RNA was fractionated on a 1.0% agarose-formaldehyde gel, transferred to a GeneScreen plus membrane (NEN), then hybridized with 32P-labeled murine IL-15 cDNA. The translational product in the reticulocyte lysates was boiled in Laemmli buffer (14) and separated on an SDS-15% polyacrylamide gel.

Quantitation of IL-15 protein synthesis

To quantitate T cell stimulatory activity by the CTLL-2 bioassay, serial dilutions of translational products programmed with nonlabeled methionine were added to 15,000 washed CTLL-2 cells/well. Triplicate cultures were assayed in the presence of saturating levels of anti-IL-2, -IL-4, or -IL-15 mAbs to ensure that the effect was due to IL-15. The cells were cultured for 48 h at 37°C in 5% CO2 in air, pulsed with 1 µl (0.25 µCi) of [3H]TdR (Amersham, Buckinghamshire, U.K.) to each well 24 h before harvested. After the culture period, the cells were then harvested onto glass fiber filter paper and the T cell-stimulatory activity was assessed by [3H]TdR incorporation, determined in a liquid scintillation counter.

Immunoprecipitation assays

Peritoneal macrophages were cultured with 100 U/ml IFN-{gamma}, 5 µg/ml LPS, and 100 µCi/ml [35S]methionine in methionine-free MEM without FBS for 6 h at 37°C. After three washes with PBS, macrophages were lysed by immunoprecipitation buffer A (10 mM Tris-HCl, 1% Nonidet P-40, 0.15 M NaCl, 1 mM EDTA, and 10 µg/ml aprotinin). Five micrograms of anti-murine IL-15 mAb (rat IgG, PharMingen) or isotype control rat IgG were added to 200 µl of lysate. After an incubation at 4°C for 60 min, 40 µl of protein G-Sepharose 4 Fast Flow (Pharmacia Biotech) was added. After incubation at 4°C for 60 min, the immune complexes were precipitated by centrifugation and washed five times with buffer A. Associated proteins were eluted by boiling in Laemmli buffer (14) and separated on an SDS-15% polyacrylamide gel.


    Results
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Cloning of murine IL-15 cDNA isoforms generated by alternative splicing

We reported that the expression level of IL-15 mRNA in macrophages increased progressively 6 h after infection with Salmonella choleraesuis in mice as assessed by RT-PCR with specific primers for exons 6 and 8 (4). To clone the full length cDNA of murine IL-15, the cDNA from macrophages stimulated with LPS for 6 h was amplified by PCR with specific primers for exons 1 and 8 in the untranslated region of IL-15 cDNA, and the amplified products were hybridized with an internal probe for exon 7. As shown in Figure 1Go, RT-PCR using primers for exons 1 and 8 demonstrated two transcripts in macrophages stimulated with LPS, while exons 6 and 8 of the translated region showed a single band (4) (data not shown). These two amplified products differed by approximately 120 bp (710 bp and 830 bp). The expression of these transcripts increased equally 6 h after stimulation with LPS.



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FIGURE 1. Expression of IL-15 mRNA in J774A.1 macrophages after stimulation with LPS. J774A.1 macrophages (105 cells) were cultured with LPS (5 µg/ml) for 1, 3, or 6 h. Total RNA extracted from the stimulated macrophages at the indicated times was reverse transcribed into cDNA and amplified by PCR using specific primers for exons 1 and 8 of IL-15 cDNA. Southern blots of PCR products were hybridized with an internal probe specific for exon 7. Radioactivity of the blots was analyzed quantitatively using Fujix BAS 2000 Bio-Image Analyzer (Fuji Photo Film Co.). Raw data of radio activity are presented as PSL/area (mm2).

 
To examine the nucleotide sequences of the IL-15 mRNA in macrophages stimulated with LPS, the RT-PCR products were cloned into the TA cloning vector PCR II and the nucleotide sequences of 13 clones were determined. Three typical isoforms were found in the IL-15 transcripts. Among the 13 clones, 6 had the typical IL-15 cDNA sequences containing all 8 exons as reported (Fig. 2GoA). Five clones had the exon 2 deleted-isoform generated by alternative splicing. The other two clones had the exon 2 deleted isoform containing an additional sequence, which we termed {phi}, between originally described exons 4 and 5.



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FIGURE 2. A, cDNA sequence of IL-15 in macrophages stimulated with LPS. The RT-PCR product of cDNA derived from J774A.1 macrophages cultured with LPS (5 µg/ml) for 6 h using specific primers for exons 1 and 8 of murine IL-15 cDNA was cloned into TA vector PCR II (Invitrogen). Purified dsDNA was sequenced using a Taq Dye Primer Cycle Sequencing Kit and an ABI 373A DNA sequencer (Applied Biosystems). Underlined codons represent stop codons; translation initiation ATG are darkened and additional sequences in exon 5 are boxed. B, Genomic DNA sequence of upstream genomic DNA of exon 5. The PCR product of the genomic DNA library in the Mouse Promoter Finder DNA Walking Kit (Clontech Lab., Palo Alto, CA) using exon 5-specific primers was cloned into TA vector PCR II (Invitrogen). Purified dsDNA was sequenced using a Taq Dye Primer Cycle Sequencing Kit and an ABI 373A DNA sequencer (Applied Biosystems). The consensus AG of the splice site is shown in bold letters. Additional sequences in exon 5 are boxed. The pyrimidine-enriched stretch is underlined. C, Comparison of the predicted amino acid sequence of murine IL-15 isoform with alternative exon 5 and with originally described exon 5 in macrophages stimulated with LPS. Conserved amino acids are indicated by asterisks. Gaps have been introduced to maximize homology. D, Organization of the mouse IL-15 gene and the alternatively spliced transcripts. Exons 1 to 8 are shown as open boxes, 5' and 3' flanking sequences as lines, and introns as disconnected lines. ATG, translation initiation; {phi} denote alternatively spliced additional sequence of exon 5. Coding regions are indicated by black boxes; noncording region by stippled boxes. Open arrow head shows predicted cleavage site for mature IL-15 protein.

 
To identify the origin of the additional sequence {phi} in the IL-15 isoform, we cloned an intron between exons 4 and 5 from a genomic DNA using Promoter Finder DNA Walking Kits as described in Materials and Methods. A 2-kbp fragment amplified by specific primers for exon 5 of murine IL-15 cDNA was cloned and the nucleotide sequence was determined. The novel sequence was identical to the just upstream genomic sequence of exon 5 and upstream the novel sequence seems to have an intron termination characterized by adenine guanine (AG) splice-acceptor sequence and pyrimidine-enriched stretch although it differed by three nucleotides from consensus sequence for the 3' splice site (Fig. 2GoB). These results suggest that the alternative exon 5 with the novel sequence in the isoform was generated by an alternative splicing upstream of exon 5. Notably, five stop codons were found in the 136-bp sequence followed by a new AUG (Fig. 2GoA). The predicted IL-15 precursor isoform encoded by the new ORF contains a short leader peptide of 26 amino acids, but shares the same amino acid composition as mature IL-15 protein (Fig. 2Go, C and D). However, the new leader peptide displayed the no net charge of N-terminal basically-charged region assessed by McGeoch’s methods (15). The von Heijne signal score of the new leader peptide was too low for a signal sequence (-0.53 vs 2.03 of the original leader peptide) (16). This means the possibility of not possessing a signal sequence in the leader peptide, indicating that the shorter isoform of murine IL-15 precursor may be restricted in the cytoplasm.

In vitro transcription/translation of splicing isoforms of IL-15 mRNA

We next compared the transcriptional or translational efficiency among the IL-15 mRNA isoforms with exon 5 or alternative exon 5 using the rabbit reticulocyte translation/transcription coupled system. First, we examined the transcription level in rabbit reticulocyte lysates programmed with the splicing isoform of IL-15 cDNA by Northern hybridization using a murine IL-15 full length cDNA probe. Consistent with RT-PCR in LPS-stimulated macrophages, there seems not to be much difference in the level of in vitro transcription among three splicing isoforms as shown in Figure 3Go. We then examined the translational level of the splicing isoforms using the rabbit reticulocyte-coupled system. The translational efficiency of the exon 2-deleted isoform with normal exon 5 was 1.4-fold higher than the typical IL-15 cDNA sequence containing all eight exons as reported (20.7 kDa) (Fig. 4Go). Surprisingly, the translational efficiency of the exon 2-deleted isoform containing an alternative exon 5 between exons 4 and 5 (16.0 kDa) was 4.1-fold higher than those of IL-15 exon 2-deleted isoform with normal exon 5 (20.7 kDa) (Fig. 4Go). As expected, the molecular mass of the translation product from exon 2-deleted isoform containing an alternative exon 5 corresponded to the predicted shorter isoform of IL-15 precursor isoform encoded by the new ORF (predicted mass is 15.9 kDa). To confirm that these translational products are derived from the IL-15-coding region in the cDNA-splicing isoform, we immunoprecipitated the products with anti-murine IL-15 mAb. The immunoprecipitation profile was identical to that of the SDS-PAGE separation of the translational products (data not shown). To confirm the biologic activity of the translational products, we examined the stimulatory activity of the products by the CTLL-2 proliferation assay. The translation product programmed with the exon 2-deleted isoform containing an alternative exon 5 promoted more growth of CTLL-2 than those of the IL-15 isoform cDNA with normal exon 5, and the promoting activity was significantly inhibited by an anti-IL-15-neutralizing mAb (data not shown). These results suggested that translational efficiency is up-regulated by the alternative splicing of exon 5 in murine IL-15 mRNA.



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FIGURE 3. Northern blots of IL-15 mRNA derived from cDNA isoforms. IL-15 cDNA isoforms were cloned into the PCR III vector (Invitrogen) containing T7 promoter site and the bovine growth hormone polyadenylation signal. In vitro transcription/translation proceeded with IL-15 cDNA isoforms cloned into PCR III vectors (1 µg) using the TNT T7-coupled reticulocyte lysate system (Promega) followed [35S]methionine labeling as recommended by Promega. Total RNA was extracted from the programmed lysates with acid guanidinium thiocyanate-phenol-chloroform. RNA was fractionated on a 1.0% agarose gel (A), transferred to a GeneScreen plus membrane, then hybridized with 32P-labeled IL-15 full length cDNA (B).

 


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FIGURE 4. In vitro translation of IL-15 cDNA isoforms. IL-15 cDNA isoforms were cloned into PCR III vectors (Invitrogen) containing a T7 promoter site and the bovine growth hormone polyadenylation signal. In vitro transcription/translation proceeded with IL-15 cDNA isoforms cloned into PCR III vectors (1 µg) using the TNT T7 coupled reticulocyte lysate system (Promega) followed [35S]methionine labeling as recommended by Promega. Translational products in reticulocyte lysates were boiled in Laemmli buffer and separated on an SDS-15% polyacrylamide gel. Radioactivity of the blots was analyzed quantitatively using Fuji BAS-2000 phosphorimaging analyzer. The signal intensity is presented as relative value to radioactivity of isoform containing alternative exon 5.

 
Detection of the alternative splicing isoform in stimulated peritoneal macrophages

We showed the post-transcriptional regulation of IL-15 mRNA in LPS-stimulated J774A.1 cell line. To generalize this regulation of IL-15 secretion to conventional macrophages in mice, we examined the expression of the mRNA isoform generated by alternative splicing in peritoneal macrophages from BALB/c mice. As shown in Figure 5Go, high expression levels of isoform containing an alternative exon 5 were detected in peritoneal macrophages stimulated with IFN-{gamma}/LPS or those infected with Salmonella using specific primers for murine IL-15 exon 3 and a novel sequence within an alternative exon 5. The mRNA isoform with exon 2 (320 bp) was also predominantly expressed in peritoneal macrophages stimulated with IFN-{gamma}/LPS or infected with S. choleraesuis compared with that without exon 2 (280 bp) as assessed by specific primers for exons 1 and 4. Thus, the mRNA isoforms generated by alternative splicing were expressed in conventional macrophages after stimulation with IFN-{gamma}/LPS or by bacterial infection, but transcription of exon 2-deleted isoform containing alternative exon 5 is not predominant in the macrophages stimulated with LPS.



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FIGURE 5. Expression of IL-15 mRNA in peritoneal macrophages. Peritoneal macrophages (105 cells) of female BALB/c mice (6 wk) were cultured with Salmonella choleraesuis 31N-1, {gamma}-IFN (100 U/ml) or {gamma}-IFN/LPS (5 µg/ml) or without stimulation for 6 h. Total RNA extracted from the macrophages with or without stimulation was reverse transcribed into cDNA and amplified by PCR using a specific primers for exons of murine IL-15 cDNA. The results were analyzed by interpretive densitometer Master Scan (CSPI, Billerica, CA). The results of densitometry analysis were expressed as the integrated OD362. The results were expressed as the relative OD362 compared with the OD of isoform in nonstimulated macrophages. Data are representative of three independent experiments, and a typical results is shown.

 
We demonstrated that the alternative exon 5 in the mRNA isoform generated by alternative splicing up-regulated the translational efficiency of the IL-15 shorter isoform. The predicted IL-15 precursor encoded by the new ORF displays new short leader sequence and is restricted in cytoplasm. We next examined the presence of the shorter protein in peritoneal macrophages stimulated with IFN-{gamma}/LPS. As shown in Figure 6Go, the shorter protein that was detected in stimulated macrophages was identical to that of the in vitro translational products, with a m.w. of approximately 16 kDa. Thus, the alternative splicing upstream of exon 5 in stimulated macrophages may be closely associated with up-regulation of intracellular IL-15 production.



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FIGURE 6. Immunoprecipitation of shorter IL-15 isoform in peritoneal macrophages stimulated with IFN-{gamma}/LPS. Peritoneal macrophages of female BALB/c were cultured with 100 U/ml IFN-{gamma} and 5 µg/ml LPS, and 100 µCi/ml [35S]methionine in methionine-free MEM without FBS for at 37°C. After being lysed by immunoprecipitation buffer A, 5 µg of anti-murine IL-15 mAb ({alpha} IL-15) or isotype control rat IgG (rat IgG) were added to 200 µl of the lysate. Associated proteins eluted by boiling in Laemmli buffer were separated on an SDS-15% polyacrylamide gel.

 

    Discussion
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
In this study, we cloned murine IL-15 cDNA containing an alternative exon 5 generated by alternative splicing upstream of originally defined exon 5, from the LPS-stimulated J774 A.1 cell line. We found that the translation efficiency of the isoform containing alternative exon 5 was significantly higher than that of isoforms with exon 5. The translational product of the isoform containing alternative exon 5 had a shorter ORF due to stop codons in the additional sequence upstream of exon 5, followed by a new AUG codon, and displays a shorter leader sequence but shares the same amino acid composition as mature IL-15 protein. The shorter isoform of IL-15 precursor derived from the IL-15 mRNA isoform was also detected predominantly in peritoneal macrophages stimulated with IFN-{gamma}/LPS, which expressed an abundant level of an alternative exon 5. These results suggest that normal IL-15 production in stimulated macrophages is regulated by splicing of alternative exon 5.

Anderson et al. have reported murine genomic structure of IL-15, which consisted of eight exons spanning at least 34 kb in chromosome 8 (7). It has been recently reported that an isoform with novel exon is generated by alternative splicing in human IL-15 (17). Although the novel exon arose from 494 bp downstream of the end of exon 2 in human IL-15 mRNA, the precise location of the exon remains to be elucidated. Here we found a murine IL-15 mRNA isoform containing an additional 136-bp sequence {phi} between exons 4 and 5. Genomic sequence between exons 4 and 5 reveals that this additional sequence arose from just upstream of exon 5 and had an alternative intron termination 3' site further upstream. It would thus appear that the alternative exon 5 with additional sequence is generated by usage of the alternative 3' splice site upstream of exon 5. The alternative 3' splicing site further upstream of alternative exon 5 has three nucleotides that differ from the known consequence sequence for the 3' splice site, whereas the sequence of the 3' splice site of exon 5 differs by only one nucleotide from the consensus sequence (18). Therefore, we can speculate that the splicing at the alternative 3' splice site, being capable of producing an alternative exon 5, may be inefficient and easily skipped, thereby resulting in generation of IL-15 mRNA with normal exon 5 using the next downstream 3' splice site. The alternative splicing pathway represents a mechanism whereby diversity is generated in a reversible fashion without a requirement for the expression of a new gene (19). Changes in the alternative splicing of specific pre-mRNA molecules may be associated with unique function of each isoform. Many examples of alternative RNA splicing are used to generate various forms of mRNA in many viral and eukaryote systems (20). However, the alternative spliced internal exons we found here are uncommon in vertebrate gene and, more importantly, the uses of an alternative exon to enhance the translational efficiency is a novel mechanisms for the post-transcriptional regulation of protein synthesis. Although alternative splicing is known to be related to changes in intracellular pH, cell cycle, or tissue specificity (21), the mechanism governing alternative splicing of IL-15 remains elusive. The further analysis of mechanisms controlling internal splicing of an exon of IL-15 may provide a clue to understand how protein synthesis is regulated by an alternative splicing of RNA transcript.

It is emphasized that the presence of upstream AUGs in the 5'-UTR of mRNA dramatically reduces the efficiency of translation (22). In general, 5'-UTR of effectively translated mRNA are short and unencumbered by upstream AUGs in the initiation AUG. On analysis of human IL-15 cDNA, the 5'-UTR is long (316 bp) and includes multiple upstream AUGs (1). Bamford et al. showed that IL-15 synthesis by the adult T cell leukemia line HuT-102 involves an increase in IL-15 mRNA transcription and translation secondary to the production of the HTLV-I R element fusion message that lacks many upstream AUGs (10). This indicates that the presence of these 10 upstream AUGs interferes with IL-15 mRNA translation in humans. In the murine IL-15 sequence, there are five upstream AUGs in an unusually long 5'-untranslated region (UTR) (465 bp) (7). However, from our studies, the translational efficiency of IL-15 mRNA lacking exon 2 including three AUGs generated by alternative splicing was also inhibited at the same level as the full length IL-15 mRNA. The splicing isoform containing an alternative exon 5 showed a higher efficiency of translation and generated a shorter isoform of IL-15 precursor. This suggests that translation uses a mechanism of internal initiation on alternative exon 5, which would bypass the IL-15-impeded 5'-UTR.

A full length cDNA clone encodes a 162-amino acid precursor polypeptide containing an unusually long 48-amino acid leader sequence that is cleaved at the experimentally determined NH2-terminus to form the mature protein (1, 7). However, the translational efficiency of the mRNA was very low in vivo and in vitro, and thus secretion of the protein was only a marginal level, if any (10). Onu et al. showed that secretion clearly increases after replacing the IL-15 leader peptide with a foreign one, such as CD33 leader peptide (23). This suggests that the naive leader sequence is involved in the control of cytokine secretion. On the other hand, murine shorter IL-15 precursor encoded by alternative splicing mRNA containing alternative exon 5, which displayed high efficiency of translation, lacks hydrophobic domains of signal sequence in the leader peptide. This indicates that the shorter isoform of murine IL-15 precursor may be restricted in the cytoplasm.

We tried to examine the biologic activity of cDNA isoform containing alternative exon 5 in vivo using COS-7 cells transfected with cDNA in eukaryotic expression vector. Although the transcription of the isoform was significantly high in the transfectant, there is no activity of IL-15 in the culture supernatant using CTLL-2 assay (data not shown). This result indicates that IL-15 protein encoded by the mRNA isoform is accumulated in cytoplasm of the transfectant. However, we cannot at present define the amount of IL-15 produced in cytoplasm of the transfectant at the protein level because the Ab against mouse IL-15 is not available for immunostaining assay. Bamford et al. reported that activated purified monocytes made a large amount of IL-15 mRNA, but the IL-15 biologic activity was not demonstrable in the supernatants of such cells by biologic means and ELISA (10). However, Doherty et al. reported that culture supernatants from macrophages stimulated in the presence of IFN-{gamma} enhanced the proliferation of CTLL-2 cells, even in the presence of saturating quantities of anti-IL-2 or anti-IL-4 Ab (8). We also showed that biologically significant levels of IL-15 that stimulate {gamma}{delta} T cells are produced by macrophages infected with Salmonella choleraesuis 31N-1, because {gamma}{delta} T cells produced IFN-{gamma} in response to J774A.1, which expressed abundant levels of IL-15 mRNA, the production of which was inhibited significantly by anti-IL-15 Ab (4). We presently do not understand the reason for this discrepancy. It is possible to build up one hypothesis that a specific stimulus is needed to induce secretion of IL-15 after accumulation of intracellular IL-15 precursor. This suggests that the mechanism of IL-15 secretion is distinct from the typical secretory proteins, and may present a novel pathway of protein secretion, such as the mechanism of IL-1 or IFN-{gamma}-inducing factor secretion (24, 25, 26).

In conclusion, we cloned various forms of murine IL-15 cDNA generated by alternative splicing and showed that the translation efficiency of the isoform-containing alternative exon 5 was significantly higher than those of splicing isoforms with normal exon 5. The shorter isoform of the IL-15 precursor was predominantly detected in peritoneal macrophages stimulated with IFN-{gamma}/LPS, which expressed an abundant level of an alternative exon 5. These results suggest that normal IL-15 production in stimulated macrophages is regulated by splicing of alternative exon 5.


    Footnotes
 
1 This work was supported in part by a grant to H.N. from the Ministry of Education, Science and Culture of the Japanese Government, the Aichi Cancer Research Foundation, a Searle Scientific Research Fellowship, the Ciba-Geigy Foundation (Japan) for the Promotion of Science, and the Yokoyama Research Foundation. This work was also supported in part by a grant to Y.Y. from the Ministry of Education, Science and Culture, the Ministry of Health Welfare of the Japanese government. Back

2 Address correspondence and reprint requests to Dr. Hitoshi Nishimura, Laboratory of Host Defense and Germfree Life, Research Institute for Disease Mechanism and Control, Nagoya University School of Medicine, Nagoya 466, Japan. Back

3 Abbreviations used in this paper: HTLV-I, human T cell lymphotropic virus type I; AUG, adenine uracil guanine; PEC, peritoneal exuded cells; ORF, open reading frame; UTR, untranslated region; PSL, photo-stimulated luminescence value. Back

Received for publication May 9, 1997. Accepted for publication October 1, 1997.


    References
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 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 

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