Microtubule-associated coiled-coil protein Ssm4 is involved in the meiotic development in fission yeast

Structural insights reveal the specific recognition of meiRNA by the Mei2 protein

In the fission yeast Schizosaccharomyces pombe, Mei2, an RNA-binding protein essential for entry into meiosis, regulates meiosis initiation. Mei2 binds to a specific non-coding RNA species, meiRNA, and accumulates at sme2 gene locus, which encodes meiRNA. Previous research has shown that the Mei2 C-terminal RNA recognition motif (RRM3) physically interacts with meiRNA 5' region in vitro and stimulates meiosis in vivo. However, the underlying mechanism still remains elusive. We first employed an in vitro crosslinking and immunoprecipitation sequencing (CLIP-seq) assay and demonstrated a preference for U-rich motifs of meiRNA by Mei2 RRM3. We then solved the crystal structures of Mei2 RRM3 in the apo form and complex with an 8mer RNA fragment, derived from meiRNA, as detected by in vitro CLIP-seq. These results provide structural insights into Mei2 RRM3-meiRNA complex and reveal that Mei2 RRM3 binds specifically to the UUC(U) sequence. Furthermore, a structure-based Mei2 mutation, Mei2F644A causes defective karyogamy, suggesting an essential role of the RNA-binding ability of Mei2 in regulating meiosis.

Tell the Difference Between Mitosis and Meiosis: Interplay Between Chromosomes, Cytoskeleton, and Cell Cycle Regulation

Meiosis is a specialized style of cell division conserved in eukaryotes, particularly designed for the production of gametes. A huge number of studies to date have demonstrated how chromosomes behave and how meiotic events are controlled. Yeast substantially contributed to the understanding of the molecular mechanisms of meiosis in the past decades. Recently, evidence began to accumulate to draw a perspective landscape showing that chromosomes and microtubules are mutually influenced: microtubules regulate chromosomes, whereas chromosomes also regulate microtubule behaviors. Here we focus on lessons from recent advancement in genetical and cytological studies of the fission yeast Schizosaccharomyces pombe, revealing how chromosomes, cytoskeleton, and cell cycle progression are organized and particularly how these are differentiated in mitosis and meiosis. These studies illuminate that meiosis is strategically designed to fulfill two missions: faithful segregation of genetic materials and production of genetic diversity in descendants through elaboration by meiosis-specific factors in collaboration with general factors.

meiRNA, A Polyvalent Player in Fission Yeast Meiosis

A growing number of recent studies have revealed that non-coding RNAs play a wide variety of roles beyond expectation. A lot of non-coding RNAs have been shown to function by forming intracellular structures either in the nucleus or the cytoplasm. In the fission yeast Schizosaccharomyces pombe, a non-coding RNA termed meiRNA has been shown to play multiple vital roles in the course of meiosis. meiRNA is tethered to its genetic locus after transcription and forms a peculiar intranuclear dot structure. It ensures stable expression of meiotic genes in cooperation with an RNA-binding protein Mei2. Chromosome-associated meiRNA also facilitates recognition of homologous chromosome loci and induces robust pairing. In this review, the quarter-century history of meiRNA, from its identification to functional characterization, will be outlined.

The kinetochore protein Kis1/Eic1/Mis19 ensures the integrity of mitotic spindles through maintenance of kinetochore factors Mis6/CENP-I and CENP-A

Microtubules play multiple roles in a wide range of cellular phenomena, including cell polarity establishment and chromosome segregation. A number of microtubule regulators have been identified, including microtubule-associated proteins and kinases, and knowledge of these factors has contributed to our molecular understanding of microtubule regulation of each relevant cellular process. The known regulators, however, are insufficient to explain how those processes are linked to one another, underscoring the need to identify additional regulators. To find such novel mechanisms and microtubule regulators, we performed a screen that combined genetics and microscopy for fission yeast mutants defective in microtubule organization. We isolated approximately 900 mutants showing defects in either microtubule organization or the nuclear envelope, and these mutants were classified into 12 categories. We particularly focused on one mutant, kis1, which displayed spindle defects in early mitosis. The kis1 mutant frequently failed to assemble a normal bipolar spindle. The responsible gene encoded a kinetochore protein, Mis19 (also known as Eic1), which localized to the interface of kinetochores and spindle poles. We also found that the inner kinetochore proteins Mis6/CENP-I and Cnp1/CENP-A were delocalized from kinetochores in the kis1 cells and that kinetochore-microtubule attachment was defective. Another mutant, mis6, also displayed similar spindle defects. We conclude that Kis1 is required for inner kinetochore organization, through which Kis1 ensures kinetochore-microtubule attachment and spindle integrity. Thus, we propose an unexpected relationship between inner kinetochore organization and spindle integrity.

Hexanucleotide motifs mediate recruitment of the RNA elimination machinery to silent meiotic genes

The selective elimination system blocks the accumulation of meiosis-specific mRNAs during the mitotic cell cycle in fission yeast. These mRNAs harbour a region, the determinant of selective removal (DSR), which is recognized by a YTH-family RNA-binding protein, Mmi1. Mmi1 directs target transcripts to destruction in association with nuclear exosomes. Hence, the interaction between DSR and Mmi1 is crucial to discriminate mitosis from meiosis. Here, we show that Mmi1 interacts with repeats of the hexanucleotide U(U/C)AAAC that are enriched in the DSR. Disruption of this ‘DSR core motif’ in a target mRNA inhibits its elimination. Tandem repeats of the motif can function as an artificial DSR. Mmi1 binds to it in vitro. Thus, a core motif cluster is responsible for the DSR activity. Furthermore, certain variant hexanucleotide motifs can augment the function of the DSR core motif. Notably, meiRNA, which composes the nuclear Mei2 dot required to suppress Mmi1 activity during meiosis, carries numerous copies of the core/augmenting motifs on its tail and is indeed degraded by the Mmi1/exosome system, indicating its likely role as decoy bait for Mmi1.

A novel factor Iss10 regulates Mmi1-mediated selective elimination of meiotic transcripts

A number of meiosis-specific transcripts are selectively eliminated during the mitotic cell cycle in fission yeast. Mmi1, an RNA-binding protein, plays a crucial role in this selective elimination. Mmi1 recognizes a specific region, namely, the determinant of selective removal (DSR) on meiotic transcripts and induces nuclear exosome-mediated elimination. During meiosis, Mmi1 is sequestered by a chromosome-associated dot structure, Mei2 dot, allowing meiosis-specific transcripts to be stably expressed. Red1, a zinc-finger protein, is also known to participate in the Mmi1/DSR elimination system, although its molecular function has remained elusive. To uncover the detailed molecular mechanisms underlying the Mmi1/DSR elimination system, we sought to identify factors that interact genetically with Mmi1. Here, we show that one of the identified factors, Iss10, is involved in the Mmi1/DSR system by regulating the interaction between Mmi1 and Red1. In cells lacking Iss10, association of Red1 with Mmi1 is severely impaired, and target transcripts of Mmi1 are ectopically expressed in the mitotic cycle. During meiosis, Iss10 is downregulated, resulting in dissociation of Red1 from Mmi1 and subsequent suppression of Mmi1 activity.

The fission yeast stress-responsive MAPK pathway promotes meiosis via the phosphorylation of Pol II CTD in response to environmental and feedback cues

The RRM-type RNA-binding protein Mei2 is a master regulator of meiosis in fission yeast, in which it stabilizes meiosis-specific mRNAs by blocking their destruction. Artificial activation of Mei2 can provoke the entire meiotic process, and it is suspected that Mei2 may do more than the stabilization of meiosis-specific mRNAs. In our current study using a new screening system, we show that Mei2 genetically interacts with subunits of CTDK-I, which phosphorylates serine-2 residues on the C-terminal domain of RNA polymerase II (Pol II CTD). Phosphorylation of CTD Ser-2 is essential to enable the robust transcription of ste11, which encodes an HMG-type transcription factor that regulates the expression of mei2 and other genes necessary for sexual development. CTD Ser-2 phosphorylation increases under nitrogen starvation, and the stress-responsive MAP kinase pathway, mediated by Wis1 MAPKK and Sty1 MAPK, is critical for this stress response. Sty1 phosphorylates Lsk1, the catalytic subunit of CTDK-I. Furthermore, a feedback loop stemming from activated Mei2 to Win1 and Wis4 MAPKKKs operates in this pathway and eventually enhances CTD Ser-2 phosphorylation and ste11 transcription. Hence, in addition to starting meiosis, Mei2 functions to reinforce the commitment to it, once cells have entered this process. This study also demonstrates clearly that the stress-responsive MAP kinase pathway can modulates gene expression through phosphorylation of Pol II CTD.

Hundreds of genes are newly expressed during meiosis, a process to form gametes, and the control of meiosis-specific gene expression is not simple. The master regulator of meiosis in fission yeast, Mei2, blocks an RNA destruction system that selectively degrades meiosis-specific mRNAs, highlighting the importance of post-transcriptional control in meiotic gene expression. Here we present another example of unforeseen regulation for meiosis. Ste11 is a key transcription factor responsible for the early meiotic gene expression in fission yeast. The ste11 gene is transcribed robustly only when serine-2 residues on the C-terminal domain (CTD Ser-2) of RNA polymerase II are phosphorylated. We show that the stress-responsive MAP kinase cascade transmits the environmental signal to stimulate CTD Ser-2 phosphorylation. Sty1 MAP kinase appears to phosphorylate and activate the catalytic subunit of CTDK-I, which in turn phosphorylates CTD Ser-2. We demonstrate further that Mei2, expression of which depends on Ste11, can activate the MAP kinase cascade, forming a feedback loop. Thus, we clarify here three important issues in cellular development: the physiological role of CTD Ser-2 phosphorylation, the molecular function of the stress-responsive MAP kinase pathway, and the presence of positive feedback that reinforces the commitment to meiosis.

Caenorhabditis elegans ortholog of the p24/p22 subunit, DNC-3, is essential for the formation of the dynactin complex by bridging DNC-1/p150(Glued) and DNC-2/dynamitin

Dynactin is a multisubunit protein complex required for the activity of cytoplasmic dynein. In Caenorhabditis elegans, although 10 of the 11 dynactin subunits were identified based on the sequence similarities to their orthologs, the p24/p22 subunit has not been detected in the genome. Here, we demonstrate that DNC-3 (W10G11.20) is the functional counterpart of the p24/p22 subunit in C. elegans. RNAi phenotypes and subcellular localization of DNC-3 in early C. elegans embryos were nearly identical to those of the known dynactin components. All other dynactin subunits were co-immunoprecipitated with DNC-3, indicating that DNC-3 is a core component of dynactin. Furthermore, the overall secondary structure of DNC-3 resembles to those of the mammalian and yeast p24/p22. We found that DNC-3 is required for the localization of the DNC-1/p150(Glued) and DNC-2/dynamitin, the two components of the projection arm of dynactin, to the nuclear envelope of meiotic nuclei in the adult gonad. Moreover, DNC-3 physically interacted with DNC-1 and DNC-2 and significantly enhanced the binding ability between DNC-1 and DNC-2 in vitro. These results suggest that DNC-3 is essential for the formation of the projection arm subcomplex of dynactin.

Contribution of dynein light intermediate and intermediate chains to subcellular localization of the dynein-dynactin motor complex in Schizosaccharomyces pombe

In fission yeast Schizosaccharomyces pombe, cytoplasmic dynein drives oscillatory nuclear movement during meiotic prophase, which may facilitate pairing of homologous chromosomes. Here, we report the identification of a dynein light intermediate chain (LIC) in fission yeast, termed Dli1p, and show that Dli1p and dynein intermediate chain (IC) Dic1p are essential for the appropriate subcellular localization and proper function of dynein during meiotic prophase. Expression of both the dli1 and dic1 genes was observed only in cells undergoing meiosis. Dli1p interacted and colocalized with dynein heavy chain Dhc1p. The subcellular localization of Dli1p was dependent on Dhc1p, and vice versa. The Dhc1p-Dli1p subcomplex could localize to the spindle pole body (SPB) with no aid of Dic1p and dynactin subunit Ssm4p, but its localization to microtubules was dependent on these two proteins. Dic1p localized to microtubules depending on Ssm4p, but not on Dhc1p and Dli1p. Its localization to the SPB, however, was dependent on Dhc1p and Dli1p. Localization of Ssm4p to the SPB was largely dependent on Dhc1p, Dli1p and Dic1p. Thus, Dli1p and Dic1p contribute differently in localizing the dynein-dynactin motor complex to organelles, providing novel insight into the in vivo function of dynein subunits in fission yeast.

Structural diversity and dynamics of genomic replication origins in Schizosaccharomyces pombe

DNA replication origins (ORI) in Schizosaccharomyces pombe colocalize with adenine and thymine (A+T)-rich regions, and earlier analyses have established a size from 0.5 to over 3 kb for a DNA fragment to drive replication in plasmid assays. We have asked what are the requirements for ORI function in the chromosomal context. By designing artificial ORIs, we have found that A+T-rich fragments as short as 100 bp without homology to S. pombe DNA are able to initiate replication in the genome. On the other hand, functional dissection of endogenous ORIs has revealed that some of them span a few kilobases and include several modules that may be as short as 25-30 contiguous A+Ts capable of initiating replication from ectopic chromosome positions. The search for elements with these characteristics across the genome has uncovered an earlier unnoticed class of low-efficiency ORIs that fire late during S phase. These results indicate that ORI specification and dynamics varies widely in S. pombe, ranging from very short elements to large regions reminiscent of replication initiation zones in mammals.

The selective elimination of messenger RNA underlies the mitosis-meiosis switch in fission yeast

The cellular programs for meiosis and mitosis must be strictly distinguished but the mechanisms controlling the entry to meiosis remain largely elusive in higher organisms. In contrast, recent analyses in yeast have shed new light on the mechanisms underlying the mitosis-meiosis switch. In this review, the current understanding of these mechanisms in the fission yeast Schizosaccharomyces pombe is discussed. Meiosis-inducing signals in this microbe emanating from environmental conditions including the nutrient status converge on the activity of an RRM-type RNA-binding protein, Mei2. This protein plays pivotal roles in both the induction and progression of meiosis and has now been found to govern the meiotic program in a quite unexpected manner. Fission yeast contains an RNA degradation system that selectively eliminates meiosis-specific mRNAs during the mitotic cell cycle. Mmi1, a novel RNA-binding protein of the YTH-family, is essential for this process. Mei2 tethers Mmi1 and thereby stabilizes the transcripts necessary for the progression of meiosis.

Meiosis specific coiled-coil proteins in Shizosaccharomyces pombe

Many meiosis-specific proteins in Schizosaccharomyces pombe contain coiled-coil motifs which play essential roles for meiotic progression. For example, the coiled-coil motifs present in Meu13 and Mcp7 are required for their function as a putative recombinase cofactor complex during meiotic recombination. Mcp6/Hrs1 and Mcp5/Num1 control horsetail chromosome movement by astral microtubule organization and anchoring dynein respectively. Dhc1 and Ssm4 are also required for horsetail chromosome movement. It is clear from these examples that the coiled-coil motif in these proteins plays an important role during the progression of cells through meiosis. However, there are still many unanswered questions on how these proteins operate. In this paper, we briefly review recent studies on the meiotic coiled-coil proteins in Sz. pombe.

Selective elimination of messenger RNA prevents an incidence of untimely meiosis

Much remains unknown about the molecular regulation of meiosis. Here we show that meiosis-specific transcripts are selectively removed if expressed during vegetative growth in fission yeast. These messenger RNAs contain a cis-acting region--which we call the DSR--that confers this removal via binding to a YTH-family protein Mmi1. Loss of Mmi1 function severely impairs cell growth owing to the untimely expression of meiotic transcripts. Microarray analysis reveals that at least a dozen such meiosis-specific transcripts are eliminated by the DSR-Mmi1 system. Mmi1 remains in the form of multiple nuclear foci during vegetative growth. At meiotic prophase these foci precipitate to a single focus, which coincides with the dot formed by the master meiosis-regulator Mei2. A meiotic arrest due to the loss of the Mei2 dot is released by a reduction in Mmi1 activity. We propose that Mei2 turns off the DSR-Mmi1 system by sequestering Mmi1 to the dot and thereby secures stable expression of meiosis-specific transcripts.

Fission yeast Num1p is a cortical factor anchoring dynein and is essential for the horse-tail nuclear movement during meiotic prophase

During meiotic prophase in the fission yeast Schizosaccharomyces pombe, the nucleus oscillates between the two ends of a cell. This oscillatory nuclear movement is important to promote accurate pairing of homologous chromosomes and requires cytoplasmic dynein. Dynein accumulates at the points where microtubule plus ends contact the cell cortex and generate a force to drive nuclear oscillation. However, it remains poorly understood how dynein associates with the cell cortex. Here we show that S. pombe Num1p functions as a cortical-anchoring factor for dynein. Num1p is expressed in a meiosis-specific manner and localized to the cell cortex through its C-terminal PH domain. The num1 deletion mutant shows microtubule dynamics comparable to that in the wild type. However, it lacks cortical accumulation of dynein and is defective in the nuclear oscillation as is the case for the dynein mutant. We also show that Num1p can recruit dynein independently of the CLIP-170 homolog Tip1p.

Mcp5, a meiotic cell cortex protein, is required for nuclear movement mediated by dynein and microtubules in fission yeast

During meiotic prophase I of the fission yeast Schizosaccharomyces pombe, oscillatory nuclear movement occurs. This promotes homologous chromosome pairing and recombination and involves cortical dynein, which plays a pivotal role by generating a pulling force with the help of an unknown dynein anchor. We show that Mcp5, the homologue of the budding yeast dynein anchor Num1, may be this putative dynein anchor. mcp5⁺ is predominantly expressed during meiotic prophase, and GFP-Mcp5 localizes at the cell cortex. Moreover, the mcp5Δ strain lacks the oscillatory nuclear movement. Accordingly, homologous pairing and recombination rates of the mcp5Δ strain are significantly reduced. Furthermore, the cortical localization of dynein heavy chain 1 appears to be reduced in mcp5Δ cells. Finally, the full function of Mcp5 requires its coiled-coil and pleckstrin homology (PH) domains. Our results suggest that Mcp5 localizes at the cell cortex through its PH domain and functions as a dynein anchor, thereby facilitating nuclear oscillation.

The p150-Glued Ssm4p regulates microtubular dynamics and nuclear movement in fission yeast

During vegetative growth of the fission yeast Schizosaccharomyces pombe, microtubules nucleate from multiple microtubule organising centres (MTOCs) close to the nucleus, polymerising until they reach the end of the cell and then shrinking back to the cell centre. In response to mating pheromone, S. pombe undergoes a morphological switch from a vegetative to a shmooing growth pattern. The switch in growth mode is paralleled by a switch in microtubular dynamics. Microtubules nucleate mostly from a single MTOC and pull on the ends of the cell to move the nucleus back and forth. This movement continues after cellular and nuclear fusion in the zygote and is important to ensure correct chromosome pairing, recombination and segregation during meiosis. Here we show that Ssm4p, a p150-Glued protein, is induced specifically in response to pheromone and is required for this nuclear movement. Ssm4p is associated with the cytoplasmic dynein complex and together with the CLIP-170 homologue Tip1p regulates dynein heavy chain localisation. We also show that Ssm4p collaborates with Tip1p in establishing the shmooing microtubular array.

Cytoplasmic dynein in fungi: insights from nuclear migration

Cytoplasmic dynein is a microtubule motor that mediates various biological processes, including nuclear migration and organelle transport, by moving on microtubules while associated with various cellular structures. The association of dynein with cellular structures and the activation of its motility are crucial steps in dynein-dependent processes. However, the mechanisms involved remain largely unknown. In fungi, dynein is required for nuclear migration. In budding yeast, nuclear migration is driven by the interaction of astral microtubules with the cell cortex; the interaction is mediated by dynein that is probably associated with the cortex. Recent studies suggest that budding yeast dynein is first recruited to microtubules, then delivered to the cortex by microtubules and finally activated by association with the cortex. Nuclear migration in many other fungi is probably driven by a similar mechanism. Recruitment of dynein to microtubules and its subsequent activation upon association with cellular structures are perhaps common to many dynein-dependent eukaryotic processes, including organelle transport.

CLIP170-like tip1p spatially organizes microtubular dynamics in fission yeast

Rod-shaped fission yeast cells grow in a polarized manner, and unlike budding yeast, the correct positioning of the growth sites at cell ends requires interphase microtubules. Here we describe a microtubule guidance mechanism that orients microtubules in the intracellular space along the long axis of the cell, guiding them to their target region at the cell ends. This mechanism involves tip1p, a CLIP170-like protein that localizes to distal tips of cytoplasmic microtubules. In the absence of tip1p, microtubular catastrophe is no longer restricted to cell ends but occurs when microtubules reach any region of the cellular cortex. Thus, tip1p enables microtubules to discriminate different cortical regions and regulates their dynamics accordingly.

Functional dissection and hierarchy of tubulin-folding cofactor homologues in fission yeast

We describe the isolation of fission yeast homologues of tubulin-folding cofactors B (Alp11) and E (Alp21), which are essential for cell viability and the maintenance of microtubules. Alp11(B) contains the glycine-rich motif (the CLIP-170 domain) involved in microtubular functions, whereas, unlike mammalian cofactor E, Alp21(E) does not. Both mammalian and yeast cofactor E, however, do contain leucine-rich repeats. Immunoprecipitation analysis shows that Alp11(B) interacts with both alpha-tubulin and Alp21(E), but not with the cofactor D homologue Alp1, whereas Alp21(E) also interacts with Alp1(D). The cellular amount of alpha-tubulin is decreased in both alp1 and alp11 mutants. Overproduction of Alp11(B) results in cell lethality and the disappearance of microtubules, which is rescued by co-overproduction of alpha-tubulin. Both full-length Alp11(B) and the C-terminal third containing the CLIP-170 domain localize in the cytoplasm, and this domain is required for efficient binding to alpha-tubulin. Deletion of alp11 is suppressed by multicopy plasmids containing either alp21(+) or alp1(+), whereas alp21 deletion is rescued by overexpression of alp1(+) but not alp11(+). Finally, the alp1 mutant is not complemented by either alp11(+) or alp21(+). The results suggest that cofactors operate in a linear pathway (Alp11(B)-Alp21(E)-Alp1(D)), each with distinct roles.

RNA-assisted nuclear transport of the meiotic regulator Mei2p in fission yeast

Fission yeast Mei2p is an RNA-binding protein required for both premeiotic DNA synthesis and meiosis I. Mei2p binds to a polyadenylated RNA molecule, meiRNA, loss of which blocks meiosis I. Mei2p forms a dot in meiotic prophase nuclei. Here, we show that meiRNA is required for the nuclear localization of Mei2p and is detectable in the dot. However, Mei2p carrying a nuclear localization signal can produce a nuclear dot and promote meiosis I in the absence of meiRNA. Mei2p expressed in cultured mammalian cells stays in the cytoplasm, but it accumulates in the nucleolus if meiRNA is coexpressed. These results indicate that meiRNA contributes to the promotion of meiosis I exclusively as a cofactor that assists nuclear transport of Mei2p.

CLIP-115, a novel brain-specific cytoplasmic linker protein, mediates the localization of dendritic lamellar bodies

Intracellular localization of organelles may depend in part on specific cytoplasmic linker proteins (CLIPs) that link membranous organelles to microtubules. Here, we characterize rat cDNAs encoding a novel, brain-specific CLIP of 115 kDa. This protein contains two N-terminal microtubule-binding domains and a long coiled-coil region; it binds to microtubules and is homologous to CLIP-170, a protein mediating the binding of endosomes to microtubules. CLIP-115 is enriched in the dendritic lamellar body (DLB), a recently discovered organelle predominantly present in bulbous dendritic appendages of neurons linked by dendrodendritic gap junctions. Local microtubule depolymerization leads to a temporary reduction of DLBs. These results suggest that CLIP-115 operates in the control of brain-specific organelle translocations.