Functional significance of nuclear export and mRNA binding of meiotic regulator Spo5 in fission yeast
© Togashi et al.; licensee BioMed Central Ltd. 2014
Received: 18 November 2013
Accepted: 3 July 2014
Published: 15 July 2014
Meiotic cells undergo two rounds of nuclear division and generate gametes. Previous studies have indicated that a number of transcription factors modulate the transcriptome in successive waves during meiosis and spore formation in fission yeast. However, the mechanisms underlying the post-transcriptional regulation in meiosis are not fully understood. The fission yeast spo5 + gene encodes a meiosis-specific RNA-binding protein, which is required for the progression of meiosis II and spore formation. However, the target RNA molecules of Spo5 are yet to be identified. Characterization of meiosis-specific RNA-binding proteins will provide insight into how post-transcriptional regulation influence gene expression during sexual differentiation.
To assess the functional significance of RNA-recognition motifs (RRMs) of Spo5, we constructed a series of new spo5 truncated mutants and previously reported spo5 missense mutants. In addition, we isolated novel spo5 missense mutants. The phenotypic characteristics of these mutants indicated that the RRMs are essential for both the localization and function of the protein. Interestingly, Spo5 is exported from the nucleus to the cytoplasm via the Rae1-dependent mRNA export pathway, but is unlikely to be involved in global mRNA export. Furthermore, cytoplasmic localization of Spo5 is important for its function, which suggests the involvement of Spo5 in post-transcriptional regulation. We identified pcr1 + mRNA as one of the critical targets of Spo5. The pcr1 + gene encodes an activating transcription factor/cAMP response element binding (ATF/CREB) transcription factor family. Among the four family members, namely Pcr1, Atf1, Atf21, and Atf31, only the mRNA encoding Pcr1 binds to Spo5.
Spo5 is exported from the nucleus with mRNAs via the Rae1-dependent pathway. RRMs are necessary for this process and also for the function of Spo5 after the nuclear export. Spo5 appears to influence the activity of pcr1 + mRNA, and the mechanism of how Spo5 stimulates the mRNA to promote the progression of meiosis II and spore formation remains an intriguing question for future research.
Meiosis is a specialized cell division process, which includes premeiotic DNA synthesis, DNA recombination followed by two rounds of cell division, and gametogenesis [1–4]. It has been shown in the fission yeast Schizosaccharomyces pombe[5–8] and the budding yeast Saccharomyces cerevisiae[1, 9–12] that a number of transcription factors dramatically modulate the transcriptome to facilitate meiosis, thereby playing critical roles in meiotic progression and sporulation (gametogenesis). In addition to transcriptional regulation, post-transcriptional regulation plays a fundamental role in the progression of meiosis and gametogenesis in higher eukaryotes. For example, cessation of transcription followed by complex translational activation and repression of stored maternal mRNAs occurs in Xenopus oocytes during meiotic progression (oocyte maturation) . In fission yeast, a specialized regulation of meiosis, called selective elimination of meiosis-specific mRNAs, facilitates the post-transcriptional degradation of meiotic mRNAs during the mitotic cell cycle . We were interested in elucidating any additional post-transcriptional regulation that might contribute to the dynamic changes observed in gene expression during meiosis in the fission yeast.
The spo5 mutant was isolated as a sporulation-deficient mutant in the original genetic screen of defective mutants in meiotic progression and/or sporulation, performed nearly half a century ago . Previous studies have indicated that the spo5 + gene encodes a meiosis-specific RNA-binding protein, carrying two RNA-recognition motifs (RRMs) in the C-terminal part (aas 192–567), and regulates the progression of meiosis II and spore formation [16–20]. Although it seems apparent that Spo5 plays an essential role to coordinate meiosis and sporulation, controlling a number of targets, the RNA molecules that bind to Spo5 have not yet been identified, except for our recent finding that cdc13 + mRNA, encoding cyclin B, can do so . Because Spo5 is likely to be involved in post-transcriptional events during meiosis, such as pre-mRNA processing, mRNA export, translation, and mRNA degradation, we analyzed this RNA-binding protein to evaluate its functions.
In this report, we demonstrate that the RRMs on Spo5 are essential for its cytoplasmic localization, where it exerts its function. Spo5 appears to be exported from the nucleus to the cytoplasm through the Rae1-dependent mRNA export pathway, but is unlikely to be involved in general mRNA export. We also show that one of the critical target RNA molecules for Spo5 is pcr1 + mRNA. Pcr1 belongs to the ATF/CREB family of transcription factors, which consists of four members in fission yeast: Pcr1, Atf1, Atf21, and Atf31. The functional relationship between Spo5 and Pcr1 is also analyzed.
Results and discussion
RNA recognition motifs are essential for the localization and function of Spo5
To clarify whether RNA-binding is required for Spo5 localization and function, we introduced missense mutations to the conserved motifs in RRMs. We constructed mutant strains that were similar to the F341A and F427A mutations previously analyzed by Kasama and colleagues . All of the mutant proteins, namely Spo5(F341A)–GFP, Spo5(F427A)–GFP, and Spo5(F341A, F427A)–GFP, accumulated in the nucleus, as did the RRM-truncated proteins (Figure 1C). These mutants were also deficient in sporulation (Figure 1D). Similar, or slightly lower production of Spo5(F341A, F427A) protein compared to the wild-type was confirmed (Additional file 1: Figure S1). The nuclear localization of these mutated Spo5-GFP proteins in our study was somewhat different from that observed in the previous study, which reported that Spo5(F341A, F427A)-GFP shows a punctate distribution in both the cytoplasm and nucleus . Our precise analysis suggested that Spo5(F341A, F427A) protein might exhibit punctate cytoplasmic distribution during early meiotic stages such as the horsetail-movement and one-nucleus stages (Additional file 2: Figure S2). The apparent difference in localization may also reflect changes in the strain construction: In the previous study, the spo5 mutant allele was integrated into the chromosomal leu1 locus, whereas the mutant allele was integrated in the authentic spo5 locus in our case. However, the actual reasons remain unclear.
We also performed a genetic screen for novel missense mutants of spo5 that were defective in meiosis and sporulation, and isolated more than ten different mutants including spo5(F341L) and spo5(S365P), both of which contained a mutation in the RRM domain. When assayed at 30°C, Spo5(F341L)–GFP accumulated in the nucleus as did Spo5(F341A)–GFP, but Spo5(S365P)–GFP did not, showing a unique phenotype (Figure 1C). Because aromatic residues in the RRM, such as F341, have been shown to interact directly with RNA , we speculated that the RNA-binding of Spo5 might be important for its cytoplasmic localization.
Spo5 localizes to the cytoplasm via the mRNA export pathway
Next, we investigated the possible involvement of the exportin-mediated mRNA export pathway  in the localization of Spo5. Ran GTPase is known as the major organizer of importin/exportin-mediated nucleocytoplasmic transport . When the Ran–exportin nuclear export pathway was blocked with leptomycin B (LMB), a potent inhibitor of exportin/Crm1 , Spo5–GFP remained in the cytoplasm (Figure 2D), demonstrating that exportin/Crm1 is dispensable for the export of Spo5.
To examine whether Spo5 itself is a component of the mRNA transport machinery, we monitored the localization of the poly (A)-binding protein (Pabp), which has been shown to accumulate in the nucleus in the rae1-167 mutant . Pabp–GFP was found to localize in the cytoplasm in spo5∆ cells (Figure 2E), suggesting that Spo5 is not an mRNA export factor.
Taken together, we conclude that Spo5 is exported to the cytoplasm via the mRNA export machinery, but is unlikely to be involved in global mRNA export. It was recently shown that Drosophila RAE1 plays an essential role in male meiosis and spermatogenesis . Fission yeast Rae1 may also promote meiosis by transporting mRNPs from the nucleus to the cytoplasm. Some RNA-binding proteins are also known to be exported to the cytoplasm through binding to mRNAs [31–33]. The mRNA-dependent nuclear export of RNA-binding proteins may emerge as a more universal phenomenon among eukaryotes than previously anticipated.
Nuclear export is important for the function of Spo5
The findings of this study indicated that mutations in RRMs caused abnormal nuclear accumulation and loss of function of Spo5. This suggests that the mRNA-dependent nuclear export of Spo5 is required for its function, although it is also possible that the loss of RNA-binding in Spo5 resulted in its abnormal localization as a secondary effect. Hence, we employed two approaches to investigate whether the nuclear export of Spo5 is a fundamental requirement for its function.
Second, we investigated whether artificial nuclear export of Spo5 could suppress sporulation defects in some spo5 mutants. Removal of RRM1 caused nuclear accumulation of Spo5 and sporulation defects, although a small portion of spo5 RRM1∆ cells could sporulate (Figure 1A,B). The fusion of a nuclear export signal (NES) to Spo5RRM1∆ (Spo5RRM1∆ –NES–GFP) enhanced its localization to the cytoplasm (Figure 3D). However, the sporulation efficiency was much lower than that observed for Spo5–GFP carrying intact RRM1, and was only comparable to that observed for Spo5RRM1∆ -GFP (Figure 3E). Hence, we conclude that the RNA-binding activity of Spo5 is necessary not only for nuclear export of the Spo5–mRNA complex via the mRNA export machinery, but also for the function of Spo5 in the cytoplasm.
pcr1 + mRNA is one of the critical targets of Spo5
The spo5(S365P) mutant isolated in this study was unique in that it did not accumulate Spo5(S365P) protein efficiently in the nucleus in rae1-167 mutant cells at the restrictive temperature (Additional file 3: Figure S3A), although it was produced in a comparable or slightly lower amount to the wild-type (Additional file 1: Figure S1), implying that this mutant protein might be defective in nuclear import. In addition, the spo5(S365P) mutant was less leaky compared to the spo5(F341L) mutant, which sporulated almost normally at 25°C, as indicated by iodine staining  and microscopic measurement (Additional file 3: Figure S3B, C). Therefore, we screened for multi-copy suppressors of spo5(S365P), expecting to identify novel candidates. We introduced the cDNA library to the spo5(S365P) mutant and picked up iodine-positive colonies. In this screening we obtained clones encoding transcription factors. Among them was the pcr1 + gene, which encodes an ATF/CREB family transcription factor. The pcr1 + gene was not a novel candidate, because we have previously reported the isolation of this gene as a multicopy suppressor of the spo5 mutant . We and others have characterized Pcr1, which is now known to form a heterodimer with Atf1 and binds to the ade6-M26 meiotic recombination hotspot [35, 36].
S. pombe has four ATF/CREB family proteins, namely Pcr1, Atf1, Atf21, and Atf31 . Although we examined all of them, only Pcr1 could suppress sporulation defects of spo5∆ cells when overexpressed (Figure 4C). Curiously, overexpression of Atf1, a functional partner that forms a heterodimer with Pcr1 , failed to suppress spo5 mutants. This suggested that Spo5 might be specifically related to pcr1 + gene expression, and furthermore, that Pcr1 might promote transcription of some meiotic genes that are regulated by Spo5. It was also evident that Spo5 could regulate factors other than Pcr1 that are important for meiotic progression and sporulation, because Pcr1 could not suppress sporulation defects of spo5∆ as efficiently as Spo5 itself (Additional file 4: Figure S4B), although pcr1 + overexpression increased the amount of pcr1 + mRNA in spo5∆ cells to a higher level than spo5 + overexpression (Additional file 4: Figure S4C). Indeed, we have recently demonstrated that Spo5 is necessary to maintain proper expression of cyclin Cdc13 .
The findings of this study indicated that Spo5 is exported to the cytoplasm via the mRNA export machinery, but not via the Ran–exportin/Crm1 system. The binding of Spo5 to mRNAs through its two RRMs appears to enable its nuclear export, and this RNA-binding activity is essential not only for the nuclear export, but also for its function in the cytoplasm. Spo5 is unlikely to be involved in general mRNA export, suggesting that it may instead be involved in the post-transcriptional regulation occurring in the cytoplasm, such as control of mRNA stability and/or translational initiation. Furthermore, we identified a novel binding target of Spo5, pcr1 + mRNA. Overexpression of the pcr1 + gene suppressed the sporulation deficiency of spo5 mutants, demonstrating that pcr1 + mRNA is a critical target of Spo5. However, Pcr1 suppressed the defect in spo5∆ cells less efficiently than Spo5, suggesting that Spo5 may also regulate factors important for meiotic progression and sporulation other than Pcr1. Suppression of spo5 by overexpression of cdc13 + is also partial . Future studies are required to identify other important targets of Spo5 and the possible role that Spo5 plays in the post-transcriptional regulation of pcr1 + mRNA and other mRNAs.
Yeast strains and genetic manipulations
Strains used in this study
h 90 spo5(S365P)-GFP-kan ade6-M216 leu1 ura4
h 90 spo5(F341L)-GFP-kan ade6-M216 leu1 ura4
h 90 spo5-GFP-kan mei2-mCherry-hph ade6-M216 leu1
h 90 spo5-GFP-kan ade6-M216 leu1 ura4
h 90 spo5(S365P)-GFP-kan cut11-4mRFP-hph CFP-atb2-nat ade6-M216 leu1 ura4
h 90 spo5(1–296)-GFP-kan ade6-M216 leu1 ura4
h 90 spo5(1–366)-GFP-kan ade6-M216 leu1 ura4
h 90 spo5(1–456)-GFP-kan ade6-M216 leu1 ura4
h 90 spo5-GFP-kan cut11-4mRFP-hph CFP-atb2-nat ade6-M216 leu1 ura4
h 90 spo5(1–525)-GFP-kan ade6-M216 leu1 ura4
h 90 spo5(1–525)-GFP-kan cut11-4mRFP-hph CFP-atb2-nat ade6-M216 leu1 ura4
h 90 spo5(F341L)-GFP-kan cut11-4mRFP-hph CFP-atb2-nat ade6-M216 leu1 ura4
h 90 spo5(1–296)-GFP-kan cut11-4mRFP-hph CFP-atb2-nat ade6-M216 leu1 ura4
h 90 spo5(1–366)-GFP-kan cut11-4mRFP-hph CFP-atb2-nat ade6-M216 leu1 ura4
h 90 spo5(1–456)-GFP-kan cut11-4mRFP-hph CFP-atb2-nat ade6-M216 leu1 ura4
h 90 spo5(RRM1∆ , ∆ 297-366)-GFP-kan ade6-M216 leu1 ura4
h 90 spo5(RRM2∆ , ∆ 385-456)-GFP-kan ade6-M216 leu1 ura4
h 90 spo5(RRM1∆ , ∆ 297-366)-GFP-kan cut11-4mRFP-hph CFP-atb2-nat ade6-M216 leu1 ura4
h 90 spo5(RRM2∆ , ∆ 385-456)-GFP-kan cut11-4mRFP-hph CFP-atb2-nat ade6-M216 leu1 ura4
h + / h - spo5-GFP-kan/ spo5-GFP-kan ade6-M216/ade6-M210 leu1/leu1 ura4/ura4
h 90 spo5(S365P)-GFP-kan rae1-167 ade6-M216 leu1 ura4
Additional file 1: Figure S1
h 90 spo5::ura4 + ::spo5(F427A)-GFP-kan ade6-M216 leu1 ura4
h 90 spo5::ura4 + ade6-M216 leu1 ura4
h 90 spo5::ura4 + ::spo5(F427A)-GFP-kan cut11-4mRFP-hph CFP-atb2-nat ade6-M216 leu1 ura4
h 90 spo5::ura4 + ::spo5(F341A)-GFP-kan ade6-M216 leu1 ura4
h 90 spo5::ura4 + ::spo5(F341A, F427A)-GFP-kan ade6-M216 leu1 ura4
Figure 1D and Additional file 1: Figure S1
h 90 spo5::ura4 + ::spo5(F341A)-GFP-kan cut11-4mRFP-hph CFP-atb2-nat ade6-M216 leu1 ura4
h 90 spo5::ura4 + ::spo5(F341A, F427A)-GFP-kan cut11-4mRFP-hph CFP-atb2-nat ade6-M216 leu1 ura4
h 90 spo5-GFP-kan rae1-167 ade6-M216 leu1 ura4
Additional file 1: Figure S1
h 90 spo5 + NLS-GFP-kan ade6-M216 leu1 ura4
h 90 spo5-GFP-kan cut11-4mRFP-hph rae1-167 ade6-M216 leu1
h 90 pabp-GFP-kan spo5::ura4 + cut11-4mRFP-hph ade6-M216 leu1 ura4
h 90 spo5(S365P)-GFP-kan rae1-167 cut11-4mRFP-hph ade6-M216 leu1 ura4
Additional file 3: Figure S3A
h 90 pabp-GFP-kan rae1-167 cut11-4mRFP-hph ade6-M216 leu1 ura4
h 90 spo5(RRM1∆ ) + NES-GFP ade6-M216 leu1 ura4
h 90 spo5(RRM1∆ ) + NES-GFP cut11-4mRFP-hph ade6-M216 leu1 ura4
h + / h - ade6-M216/ade6-M210 leu1/leu1 ura4/ura4
Additional file 4: Figure S4A-C
h + / h - spo5::ura4 + /spo5::ura4 + ade6-M216/ade6-M210 leu1/leu1 ura4/ura4
Additional file 4: Figure S4A-C
To isolate novel spo5 missense mutants, the parental spo5–GFP–kan strain, in which the GFP–Tadh-kan fragment was inserted at the chromosomal spo5 + locus, was constructed. Genomic DNA was isolated from this strain, and a DNA fragment containing the entire coding region of spo5 + with GFP–Tadh1–kan genes flanked by 500-bp up- and down-stream sequences, was amplified. The amplified fragment was then subjected to error-prone PCR amplification in order to introduce random mutations to the product, using Ex Taq DNA polymerase (Takara Bio; Japan) with 40 rounds of thermal cycling. The mutagenized fragment was introduced to the homothallic (h 90) wild-type strain JY878, and colonies that conferred G418 resistance were selected. Colonies were then replica-plated to SSA plates, and those that were deficient in sporulation were chosen using iodine staining. To exclude nonsense mutants, GFP fluorescence was monitored and GFP-positive colonies were selected. Standard sequencing methods (using a 3130 Genetic Analyzer; Applied Biosystems) were used to determine the mutation sites (F341L and S365P). The PrimeSTAR mutagenesis kit (Takara Bio) was used to introduce the F341A, F427A, and F341A mutations into the spo5 + gene cloned using the vector pCR2.1-TOPO (Life Technologies; CA, USA). The mutated fragments were then introduced into the spo5::ura4 + strain, in which the spo5 coding region was replaced with the ura4 + cassette. Colonies with correct inserts were selected on YEA plates containing 1 mg/mL 5-fluoro-orotic acid (5-FOA; Wako Pure Chemicals; Japan).
The plasmids containing the pcr1 + gene (pREP3–pcr1 +) and the spo5 + gene (pREP3–spo5 +) were isolated from a cDNA library. The pREP1 plasmids carrying the atf1 +, atf21 +, and atf31 + genes were a gift from Takatomi Yamada , and we subsequently replaced their nmt1 promoters with the nmt81 promoter.
An Axioplan2 fluorescence microscope (Zeiss; Germany) equipped with a CoolSNAP HQ2 CCD camera (Photometrics; AZ, USA) and SlideBook software (Leeds Precision; MN, USA) were used to acquire the images presented in Figures 2, 3A,B and 4A, Additional file 2: Figure S2 and Additional file 3: Figure S3A. Single-sectioned images along the Z-axis were captured and deconvolved. Single-cell imaging was performed using the DeltaVision-SoftWoRx system (GE Healthcare; UK) with a CoolSNAP HQ2 CCD camera, as described previously . Briefly, the cells selected for observation were mounted on a glass-bottomed dish (Matsunami Glass; Japan) precoated with lectin and filled with MM–N liquid medium. Serial-sectioned images were acquired along the Z-axis and stacked using the ‘quick projection’ algorithm in SoftWoRx.
To block the Crm1/exportin-dependent nuclear export machinery, 100 ng/mL leptomycin B (LMB)  was added to a culture of Spo5-GFP Mei2-mCherry cells. After 60 min incubation at 30°C, cells were subjected to fluorescence microscopy. Mei2-mCherry, an LMB-sensitive meiotic protein, served as a positive control .
The rae1-167 strain was a gift from Ravi Dhar . We employed this mutant to arrest mRNA export during meiosis. Cells were incubated on SPA at 25°C for 6 h, and then shifted to a restrictive temperature at 36°C for 3 h prior to microscopic observation.
Electrophoretic mobility shift assay (EMSA) of RNA
As reported previously , digoxigenin (DIG)-labeled RNA was prepared from PCR products using the DIG RNA Labeling kit (SP6/T7) (Roche). The RNA-binding reaction was performed using 2 ng of DIG-labeled RNA (control; derived from the GFP sequence, pcr1 and atf21) and 20–200 ng of either recombinant GST, GST-Spo5C (aas 192–567), or GST-Spo5C(FAFA), in 4 μL of a modified KNET buffer consisting of 20 mM KCl, 80 mM NaCl, 2 mM ethylene glycol bis-(2-aminoethylether) tetraacetic acid (EGTA), 50 mM Tris–HCl (pH7.5), 0.05% NP-40, 1 mM MgCl2, 2 mM dithiothreitol, 10% glycerol, and RNase Inhibitor (Roche). RNA with the GFP-coding sequence was used as a negative control. Samples were preincubated at room temperature with 10 μg of carrier Escherichia coli tRNA for 25 min. Labeled RNA was then added and incubated for another 25 min. Samples were analyzed using polyacrylamide gel electrophoresis and electroblotted to a GeneScreen Plus membrane (NEN) using 0.5× Tris-borate-EDTA (TBE) buffer. Signals were detected using a DIG Luminescent Detection Kit (Roche).
Diploid cells expressing Spo5-GFP were cultured in MM + N at 30°C for 15 h, shifted to MM-N (0 h, 30°C) and sampled for RNA extraction after 6 h. Detailed conditions for RNA-IP were described previously . Immunoprecipitated RNA was isolated by phenol-chloroform extraction. For immunoprecipitation, anti-GFP (Roche; GFP monoclonal antibody) and anti-HA (Abcam; 16B12, HA monoclonal antibody) were used. Reverse transcription was performed using the TaKaRa RNA PCR kit (AMV, Ver 3.0; Takara bio).
Western blotting, reverse transcription and quantitative PCR were performed according to the same protocols as we described previously . Following oligonucleotides were used in RT-qPCR: pcr1(forward) CCGAATTCTGGAGCGCAAT, pcr1(reverse) CACTCTTTCTTTTTCTGGCGAAA, act1(forward) TGAGGAGCACCCTTGCTTGT, and act1(reverse) TCTTCTCACGGTTGGATTTGG. Inhibition of mRNA transcription by 1,10-phenanthroline was carried out as described precisely by Galipon et al. .
Availability of supporting data
The data sets supporting the results of this article are included within the article and its additional files.
We are grateful to Drs. Ravi Dhar and Takatomi Yamada for providing the materials. We highly appreciate assistance of Dr. Mayumi Arata and Mr. Yuichi Shichino in quantitative experiments. This work was supported by Grants-in-Aid for Specially Promoted Research and Scientific Research (S) (to M.Y.) and for Scientific Research (C) (to A.Y.) from Japan Society for the Promotion of Science (JSPS), and Grant-in-Aid for Scientific Research on Priority Areas “Cell Proliferation Control” from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) (to M.S.). This work was also supported in part by the Global COE Program (Integrative Life Science Based on the Study of Biosignaling Mechanisms), MEXT, Japan.
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