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Shen S, Jian Y, Cai Z, Li F, Lv M, Liu Y, Wu J, Fu C, Shi Y. Structural insights reveal the specific recognition of meiRNA by the Mei2 protein. J Mol Cell Biol 2022; 14:6581319. [PMID: 35512546 PMCID: PMC9486875 DOI: 10.1093/jmcb/mjac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/05/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Siyuan Shen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Yanze Jian
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Zhaokui Cai
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fudong Li
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Mengqi Lv
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Yongrui Liu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Jihui Wu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Chuanhai Fu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
| | - Yunyu Shi
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.,MOE key Laboratory for Cellular Dynamics, University of Science & Technology of China, Hefei 230026, China
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Andric V, Nevers A, Hazra D, Auxilien S, Menant A, Graille M, Palancade B, Rougemaille M. A scaffold lncRNA shapes the mitosis to meiosis switch. Nat Commun 2021; 12:770. [PMID: 33536434 PMCID: PMC7859202 DOI: 10.1038/s41467-021-21032-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/05/2021] [Indexed: 11/09/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) contribute to the regulation of gene expression in response to intra- or extracellular signals but the underlying molecular mechanisms remain largely unexplored. Here, we identify an uncharacterized lncRNA as a central player in shaping the meiotic gene expression program in fission yeast. We report that this regulatory RNA, termed mamRNA, scaffolds the antagonistic RNA-binding proteins Mmi1 and Mei2 to ensure their reciprocal inhibition and fine tune meiotic mRNA degradation during mitotic growth. Mechanistically, mamRNA allows Mmi1 to target Mei2 for ubiquitin-mediated downregulation, and conversely enables accumulating Mei2 to impede Mmi1 activity, thereby reinforcing the mitosis to meiosis switch. These regulations also occur within a unique Mmi1-containing nuclear body, positioning mamRNA as a spatially-confined sensor of Mei2 levels. Our results thus provide a mechanistic basis for the mutual control of gametogenesis effectors and further expand our vision of the regulatory potential of lncRNAs.
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Affiliation(s)
- Vedrana Andric
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Alicia Nevers
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,University Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Ditipriya Hazra
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France.,Department of Biochemistry, Oxford University, Oxford, OX1 3QU, UK
| | - Sylvie Auxilien
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Alexandra Menant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Benoit Palancade
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Mathieu Rougemaille
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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meiRNA, A Polyvalent Player in Fission Yeast Meiosis. Noncoding RNA 2019; 5:ncrna5030045. [PMID: 31533287 PMCID: PMC6789587 DOI: 10.3390/ncrna5030045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/12/2019] [Accepted: 09/16/2019] [Indexed: 11/17/2022] Open
Abstract
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.
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Mukherjee K, Futcher B, Leatherwood J. mmi1 and rep2 mRNAs are novel RNA targets of the Mei2 RNA-binding protein during early meiosis in Schizosaccharomyces pombe. Open Biol 2018; 8:rsob.180110. [PMID: 30257894 PMCID: PMC6170507 DOI: 10.1098/rsob.180110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/28/2018] [Indexed: 11/12/2022] Open
Abstract
The RNA-binding protein Mei2 is crucial for meiosis in Schizosaccharomyces pombe. In mei2 mutants, pre-meiotic S-phase is blocked, along with meiosis. Mei2 binds a long non-coding RNA (lncRNA) called meiRNA, which is a 'sponge RNA' for the meiotic inhibitor protein Mmi1. The interaction between Mei2, meiRNA and Mmi1 protein is essential for meiosis. But mei2 mutants have stronger and different phenotypes than meiRNA mutants, since mei2Δ arrests before pre-meiotic S, while the meiRNA mutant arrests after pre-meiotic S but before meiosis. This suggests Mei2 may bind additional RNAs. To identify novel RNA targets of Mei2, which might explain how Mei2 regulates pre-meiotic S, we used RNA immunoprecipitation and cross-linking immunoprecipitation. In addition to meiRNA, we found the mRNAs for mmi1 (which encodes Mmi1) and for the S-phase transcription factor rep2 There were also three other RNAs of uncertain relevance. We suggest that at meiotic initiation, Mei2 may sequester rep2 mRNA to help allow pre-meiotic S, and then may bind both meiRNA and mmi1 mRNA to inactivate Mmi1 at two levels, the protein level (as previously known), and also the mRNA level, allowing meiosis. We call Mei2-meiRNA a 'double sponge' (i.e. binding both an mRNA and its encoded protein).
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Affiliation(s)
- Kaustav Mukherjee
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11790, USA
| | - Bruce Futcher
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11790, USA
| | - Janet Leatherwood
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11790, USA
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Simonetti F, Candelli T, Leon S, Libri D, Rougemaille M. Ubiquitination-dependent control of sexual differentiation in fission yeast. eLife 2017; 6:28046. [PMID: 28841135 PMCID: PMC5614563 DOI: 10.7554/elife.28046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/21/2017] [Indexed: 01/03/2023] Open
Abstract
In fission yeast, meiosis-specific transcripts are selectively eliminated during vegetative growth by the combined action of the YTH-family RNA-binding protein Mmi1 and the nuclear exosome. Upon nutritional starvation, the master regulator of meiosis Mei2 inactivates Mmi1, thereby allowing expression of the meiotic program. Here, we show that the E3 ubiquitin ligase subunit Not4/Mot2 of the evolutionarily conserved Ccr4-Not complex, which associates with Mmi1, promotes suppression of meiotic transcripts expression in mitotic cells. Our analyses suggest that Mot2 directs ubiquitination of Mei2 to preserve the activity of Mmi1 during vegetative growth. Importantly, Mot2 is not involved in the constitutive pathway of Mei2 turnover, but rather plays a regulatory role to limit its accumulation or inhibit its function. We propose that Mmi1 recruits the Ccr4-Not complex to counteract its own inhibitor Mei2, thereby locking the system in a stable state that ensures the repression of the meiotic program by Mmi1.
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Affiliation(s)
- Fabrizio Simonetti
- Institut Jacques Monod, Team "Metabolism and Function of RNA in the Nucleus", CNRS, UMR7592, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,Université Paris-Saclay, Gif-sur-Yvette, France
| | - Tito Candelli
- Institut Jacques Monod, Team "Metabolism and Function of RNA in the Nucleus", CNRS, UMR7592, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.,Université Paris-Saclay, Gif-sur-Yvette, France
| | - Sebastien Leon
- Institut Jacques Monod, Team "Membrane Trafficking, Ubiquitin and Signaling", CNRS, UMR9198, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Domenico Libri
- Institut Jacques Monod, Team "Metabolism and Function of RNA in the Nucleus", CNRS, UMR7592, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Mathieu Rougemaille
- Institut Jacques Monod, Team "Metabolism and Function of RNA in the Nucleus", CNRS, UMR7592, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
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Gu L, Jung HJ, Kwak KJ, Dinh SN, Kim YO, Kang H. An RRM-containing mei2-like MCT1 plays a negative role in the seed germination and seedling growth of Arabidopsis thaliana in the presence of ABA. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 109:273-279. [PMID: 27771580 DOI: 10.1016/j.plaphy.2016.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/10/2016] [Accepted: 10/12/2016] [Indexed: 05/01/2023]
Abstract
Despite an increasing understanding of the essential role of the Mei2 gene encoding an RNA-binding protein (RBP) in premeiotic DNA synthesis and meiosis in yeasts and animals, the functional roles of the mei2-like genes in plant growth and development are largely unknown. Contrary to other mei2-like RBPs that contain three RNA-recognition motifs (RRMs), the mei2 C-terminal RRM only (MCT) is unique in that it harbors only the last C-terminal RRM. Although MCTs have been implicated to play important roles in plants, their functional roles in stress responses as well as plant growth and development are still unknown. Here, we investigated the expression and functional role of MCT1 (At1g37140) in plant response to abscisic acid (ABA). Confocal analysis of MCT1-GFP-expressing plants revealed that MCT1 is localized to the nucleus. The transcript level of MCT1 was markedly increased upon ABA treatment. Analysis of MCT1-overexpressing transgenic Arabidopsis plants and artificial miRNA-mediated mct1 knockdown mutants demonstrated that MCT1 inhibited seed germination and cotyledon greening of Arabidopsis plants under ABA. The transcript levels of ABA signaling-related genes, such as ABI3, ABI4, and ABI5, were markedly increased in the MCT1-overexpressing transgenic plant. Collectively, these results suggest that ABA-upregulated MCT1 plays a negative role in Arabidopsis seed germination and seedling growth under ABA by modulating the expression of ABA signaling-related genes.
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Affiliation(s)
- Lili Gu
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea; Xinjiang Key Laboratory of Grassland Resources and Ecology, College of Grassland and Environmental Sciences, Xinjiang Agricultural University, Urumqi 830052, China
| | - Hyun Ju Jung
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Kyung Jin Kwak
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Sy Nguyen Dinh
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Yeon-Ok Kim
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea.
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7
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Togashi N, Yamashita A, Sato M, Yamamoto M. Functional significance of nuclear export and mRNA binding of meiotic regulator Spo5 in fission yeast. BMC Microbiol 2014; 14:188. [PMID: 25023750 PMCID: PMC4109790 DOI: 10.1186/1471-2180-14-188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 07/03/2014] [Indexed: 01/02/2023] Open
Abstract
Background 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. Results 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. Conclusions 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.
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Affiliation(s)
| | | | | | - Masayuki Yamamoto
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
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Abstract
Germ cell differentiation, the cellular process by which a diploid progenitor cell produces by meiotic divisions haploid cells, is conserved from the unicellular yeasts to mammals. Over the recent years, yeast germ cell differentiation process has proven to be a powerful biological system to identify and study several long noncoding RNAs (lncRNAs) that play a central role in regulating cellular differentiation by acting directly on chromatin. Remarkably, in the well-studied budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe, the lncRNA-based chromatin regulations of germ cell differentiation are quite different. In this review, we present an overview of these regulations by focusing on the mechanisms and their respective functions both in S. cerevisiae and in S. pombe. Part of these lncRNA-based chromatin regulations may be conserved in other eukaryotes and play critical roles either in the context of germ cell differentiation or, more generally, in the development of multicellular organisms.
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9
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Abstract
Whole genome transcriptomic analyses have identified large numbers of dynamically expressed long non-protein-coding RNAs (lncRNAs) in mammals and other animals whose functions are, as yet, largely unknown. Here we summarize the growing evidence that lncRNAs, like mRNAs, can be trafficked to and function in a wide variety of subcellular locations. Investigation of the subcellular distribution of lncRNAs has the potential to greatly expand our knowledge not only of the function of lncRNAs but also of cell biology by identifying previously unknown subcellular structures and novel constituents of known cellular organelles.
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10
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Jouannet V, Crespi M. Long Nonprotein-Coding RNAs in Plants. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2011; 51:179-200. [PMID: 21287139 DOI: 10.1007/978-3-642-16502-3_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In recent years, nonprotein-coding RNAs (or npcRNAs) have emerged as a major part of the eukaryotic transcriptome. Many new regulatory npcRNAs or riboregulators riboregulators have been discovered and characterized due to the advent of new genomic approaches. This growing number suggests that npcRNAs could play a more important role than previously believed and significantly contribute to the generation of evolutionary complexity in multicellular organisms. Regulatory npcRNAs range from small RNAs (si/miRNAs) to very large transcripts (or long npcRNAs) and play diverse functions in development and/or environmental stress responses. Small RNAs include an expanding number of 20-40 nt RNAs that function in the regulation of gene expression by affecting mRNA decay and translational inhibition or lead to DNA methylation and gene silencing. They generally involve double-stranded RNA or stem loops and imply transcriptional or posttranscriptional gene silencing (PTGS). RNA silencing besides small interfering RNA and microRNA, gene silencing in plants is also mediated by tasiRNAs (trans-acting siRNAs) and nat-siRNAs (natural antisense mediated siRNAs). In contrast to small RNAs, much less is known about the large and diverse population of long npcRNAs, and only a few have been implicated in diverse functions such as abiotic stress responses, nodulation and flower development, and sex chromosome-specific expression. Moreover, many long npcRNAs act as antisense transcripts or are substrates of the small RNA pathways, thus interfering with a variety of RNA-related metabolisms. An emerging hypothesis is that long npcRNAs, as shown for small si/miRNAs, integrate into ribonucleoprotein particles (RNPs) to modulate their function, localization, or stability to act on target mRNAs. As plants show a remarkable developmental plasticity to adapt their growth to changing environmental conditions, understanding how npcRNAs work may reveal novel mechanisms involved in growth control and differentiation and help to design new tools for biotechnological applications.
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Affiliation(s)
- Virginie Jouannet
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, 91198, Gif-sur-Yvette Cedex, France
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11
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Charon C, Moreno AB, Bardou F, Crespi M. Non-protein-coding RNAs and their interacting RNA-binding proteins in the plant cell nucleus. MOLECULAR PLANT 2010; 3:729-739. [PMID: 20603381 DOI: 10.1093/mp/ssq037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The complex responses of eukaryotic cells to external factors are governed by several transcriptional and post-transcriptional processes. Several of them occur in the nucleus and have been linked to the action of non-protein-coding RNAs (or npcRNAs), both long and small npcRNAs, that recently emerged as major regulators of gene expression. Regulatory npcRNAs acting in the nucleus include silencing-related RNAs, intergenic npcRNAs, natural antisense RNAs, and other aberrant RNAs resulting from the interplay between global transcription and RNA processing activities (such as Dicers and RNA-dependent polymerases). Generally, the resulting npcRNAs exert their regulatory effects through interactions with RNA-binding proteins (or RBPs) within ribonucleoprotein particles (or RNPs). A large group of RBPs are implicated in the silencing machinery through small interfering RNAs (siRNAs) and their localization suggests that several act in the nucleus to trigger epigenetic and chromatin changes at a whole-genome scale. Other nuclear RBPs interact with npcRNAs and change their localization. In the fission yeast, the RNA-binding Mei2p protein, playing pivotal roles in meiosis, interact with a meiotic npcRNA involved in its nuclear re-localization. Related processes have been identified in plants and the ENOD40 npcRNA was shown to re-localize a nuclear-speckle RBP from the nucleus to the cytoplasm in Medicago truncatula. Plant RBPs have been also implicated in RNA-mediated chromatin silencing in the FLC locus through interaction with specific antisense transcripts. In this review, we discuss the interactions between RBPs and npcRNAs in the context of nuclear-related processes and their implication in plant development and stress responses. We propose that these interactions may add a regulatory layer that modulates the interactions between the nuclear genome and the environment and, consequently, control plant developmental plasticity.
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Affiliation(s)
- Celine Charon
- University Paris-Sud, Institut de Biologie des Plantes, UMR8618, Orsay Cedex, F-91405, France
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12
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Yamamoto M. The selective elimination of messenger RNA underlies the mitosis-meiosis switch in fission yeast. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2010; 86:788-97. [PMID: 20948174 PMCID: PMC3037521 DOI: 10.2183/pjab.86.788] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
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.
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Affiliation(s)
- Masayuki Yamamoto
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan.
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13
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Nucleocytoplasmic transport of Alp7/TACC organizes spatiotemporal microtubule formation in fission yeast. EMBO Rep 2009; 10:1161-7. [PMID: 19696784 PMCID: PMC2731110 DOI: 10.1038/embor.2009.158] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 06/12/2009] [Accepted: 06/15/2009] [Indexed: 11/17/2022] Open
Abstract
Ran GTPase activates several target molecules to induce microtubule formation around the chromosomes and centrosomes. In fission yeast, in which the nuclear envelope does not break down during mitosis, Ran targets the centrosomal transforming acidic coiled-coil (TACC) protein Alp7 for spindle formation. Alp7 accumulates in the nucleus only during mitosis, although its underlying mechanism remains elusive. Here, we investigate the behaviour of Alp7 and its binding partner, Alp14/TOG, throughout the cell cycle. Interestingly, Alp7 enters the nucleus during interphase but is subsequently exported to the cytoplasm by the Exportin-dependent nuclear export machinery. The continuous nuclear export of Alp7 during interphase is essential for maintaining the array-like cytoplasmic microtubule structure. The mitosis-specific nuclear accumulation of Alp7 seems to be under the control of cyclin-dependent kinase (CDK). These results indicate that the spatiotemporal regulation of microtubule formation is established by the Alp7/TACC–Alp14/TOG complex through the coordinated interplay of Ran and CDK.
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Rymarquis LA, Kastenmayer JP, Hüttenhofer AG, Green PJ. Diamonds in the rough: mRNA-like non-coding RNAs. TRENDS IN PLANT SCIENCE 2008; 13:329-34. [PMID: 18448381 DOI: 10.1016/j.tplants.2008.02.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 02/19/2008] [Accepted: 02/21/2008] [Indexed: 05/20/2023]
Abstract
Non-coding RNAs are increasingly being identified as crucial regulators of gene expression and other cellular functions in plants. Experimental and computational methods have revealed the existence of mRNA-like non-coding RNAs (mlncRNAs), a class of non-coding RNAs that, in plants, are associated with tissue-specific expression, development and the phosphate-starvation response. Although their mechanisms of action are largely unknown, one can speculate that mlncRNAs act through secondary structures or specific sequences that bind to proteins or metabolites, or that have catalytic activity. This review summarizes the computational methods developed to identify candidate mlncRNAs, and the current experimental evidence regarding the function of several known mlncRNAs.
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Affiliation(s)
- Linda A Rymarquis
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
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15
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Abstract
Pneumocystis carinii is an opportunistic fungus causing severe pneumonia in immune-compromised hosts. Recent evidence suggests that Pneumocystis exists as separate sex types, though definitive evidence is currently lacking. These studies were undertaken to determine whether Pneumocystis maintains functional meiotic control molecules, which are required for sexual life stages in eukaryotes. Using the Pneumocystis carinii Genome Project database, two partial sequences for meiotic control molecules were detected, namely, PCRan1, a presumptive meiotic control kinase, and PCMei2, a homologue to a primary activator of meiosis in Schizosaccharomyces pombe. Rapid amplification of cDNA ends was employed to obtain the full open reading frames and to further investigate the functions of these proteins. These presumptive meiotic control molecules were most homologous to molecules present in S. pombe (52% identical and 67% homologous for PCRan1 and 75% identical and 88% homologous for PCMei2 by BLAST analysis). Heterologous expression of these Pneumocystis meiotic genes in corresponding temperature-sensitive and knockout strains of S. pombe, respectively, further verified the functions of the PCRan1 and PCMei2 proteins. These proteins were further shown to control downstream components of the meiotic pathway in S. pombe. Lastly, in vitro kinase assays were used to determine that PCRan1p phosphorylates PCMei2p. These experiments represent the first characterization of any proteins in P. carinii involved in meiosis and indicate the presence of a conserved meiotic pathway in Pneumocystis. Elucidation of this pathway will be essential in gaining a greater understanding of this important opportunistic fungal pathogen.
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Abstract
Most eukaryotic cells possess genetic potential to perform meiosis, but the vast majority of them never initiate it. The entry to meiosis is strictly regulated by developmental and environmental conditions, which vary significantly from species to species. Molecular mechanisms underlying the mitosis-meiosis decision are unclear in most organisms, except for a few model systems including fission yeast Schizosaccharomyces pombe. Nutrient limitation is a cue to the entry into meiosis in this microbe. Signals from nutrients converge on the activity of Mei2 protein, which plays pivotal roles in both induction and progression of meiosis. Here we outline the current knowledge of how a set of environmental stimuli eventually activates Mei2, and discuss how Mei2 governs the meiotic program molecularly, especially focusing on a recent finding that Mei2 antagonizes selective elimination of meiotic messenger RNAs.
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Affiliation(s)
- Yuriko Harigaya
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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Kasama T, Shigehisa A, Hirata A, Saito TT, Tougan T, Okuzaki D, Nojima H. Spo5/Mug12, a putative meiosis-specific RNA-binding protein, is essential for meiotic progression and forms Mei2 dot-like nuclear foci. EUKARYOTIC CELL 2007; 5:1301-13. [PMID: 16896214 PMCID: PMC1539142 DOI: 10.1128/ec.00099-06] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here a functional analysis of spo5(+)(mug12(+)) of Schizosaccharomyces pombe, which encodes a putative RNA-binding protein. The disruption of spo5(+) caused abnormal sporulation, generating inviable spores due to failed forespore membrane formation and the absence of a spore wall, as determined by electron microscopy. Spo5 regulates the progression of meiosis I because spo5 mutant cells display normal premeiotic DNA synthesis and the timely initiation of meiosis I but they show a delay in the peaking of cells with two nuclei, abnormal tyrosine 15 dephosphorylation of Cdc2, incomplete degradation of Cdc13, retarded formation and repair of double strand breaks, and a reduced frequency of intragenic recombination. Immunostaining showed that Spo5-green fluorescent protein (GFP) appeared in the cytoplasm at the horsetail phase, peaked around the metaphase I to anaphase I transition, and suddenly disappeared after anaphase II. Images of Spo5-GFP in living cells revealed that Spo5 forms a dot in the nucleus at prophase I that colocalized with the Mei2 dot. Unlike the Mei2 dot, however, the Spo5 dot was observed even in sme2Delta cells. Taken together, we conclude that Spo5 is a novel regulator of meiosis I and that it may function in the vicinity of the Mei2 dot.
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Affiliation(s)
- Takashi Kasama
- Department of Molecular Genetics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Harigaya Y, Tanaka H, Yamanaka S, Tanaka K, Watanabe Y, Tsutsumi C, Chikashige Y, Hiraoka Y, Yamashita A, Yamamoto M. Selective elimination of messenger RNA prevents an incidence of untimely meiosis. Nature 2006; 442:45-50. [PMID: 16823445 DOI: 10.1038/nature04881] [Citation(s) in RCA: 248] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 05/05/2006] [Indexed: 01/12/2023]
Abstract
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.
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Affiliation(s)
- Yuriko Harigaya
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan
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Kaur J, Sebastian J, Siddiqi I. The Arabidopsis-mei2-like genes play a role in meiosis and vegetative growth in Arabidopsis. THE PLANT CELL 2006; 18:545-59. [PMID: 16473967 PMCID: PMC1383632 DOI: 10.1105/tpc.105.039156] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The Arabidopsis-mei2-Like (AML) genes comprise a five-member gene family related to the mei2 gene, which is a master regulator of meiosis in Schizosaccharomyces pombe and encodes an RNA binding protein. We have analyzed the AML genes to assess their role in plant meiosis and development. All five AML genes were expressed in both vegetative and reproductive tissues. Analysis of AML1-AML5 expression at the cellular level indicated a closely similar expression pattern. In the inflorescence, expression was concentrated in the shoot apical meristem, young buds, and reproductive organ primordia. Within the reproductive organs, strong expression was observed in meiocytes and developing gametes. Functional analysis using RNA interference (RNAi) and combinations of insertion alleles revealed a role for the AML genes in meiosis, with RNAi lines and specific multiple mutant combinations displaying sterility and a range of defects in meiotic chromosome behavior. Defects in seedling growth were also observed at low penetrance. These results indicate that the AML genes play a role in meiosis as well as in vegetative growth and reveal conservation in the genetic mechanisms controlling meiosis in yeast and plants.
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Affiliation(s)
- Jagreet Kaur
- Centre for Cellular and Molecular Biology, Hyderabad 500007, India
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Shimada T, Yamashita A, Yamamoto M. The fission yeast meiotic regulator Mei2p forms a dot structure in the horse-tail nucleus in association with the sme2 locus on chromosome II. Mol Biol Cell 2003; 14:2461-9. [PMID: 12808043 PMCID: PMC194894 DOI: 10.1091/mbc.e02-11-0738] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Fission yeast Mei2p is an RNA-binding protein essential for induction of both premeiotic DNA synthesis and first meiotic division. Mei2p forms a dot structure at an apparently fixed position in the horse-tail nucleus during meiotic prophase. This dot formation requires a meiosis-specific RNA species, meiRNA, which is indispensable for meiosis I, and the emergence of the dot is an indicator of the ability of the cell to perform meiosis I. Herein, we have sought the identity of this dot. Analyses using chromosome segregation in haploid meiosis, reciprocal translocation of chromosomes, and gene translocation have led us to conclude that the Mei2p dot is in association with the sme2 gene on the short arm of chromosome II, which encodes meiRNA. Transcripts of sme2, rather than the DNA sequence of the gene, seem to be the determinant of the localization of the Mei2p dot. However, evidence suggests that the dot may not be a simple reflection of the attachment of Mei2p to meiRNA undergoing transcription. We speculate that the Mei2p dot is a specialized structure, either to foster the assembly of Mei2p and meiRNA or to perform some unidentified function indispensable for meiosis I.
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Affiliation(s)
- Tadayuki Shimada
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Japan
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Sato M, Watanabe Y, Akiyoshi Y, Yamamoto M. 14-3-3 protein interferes with the binding of RNA to the phosphorylated form of fission yeast meiotic regulator Mei2p. Curr Biol 2002; 12:141-5. [PMID: 11818066 DOI: 10.1016/s0960-9822(01)00654-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The switch from mitosis to meiosis is controlled by the Pat1(Ran1) kinase-Mei2p system in Schizosaccharomyces pombe. Mei2p promotes both premeiotic DNA synthesis and meiosis I, and its RNA binding ability is essential for these two processes. Mei2p forms a dot structure in the nucleus prior to meiosis I, aided by a specific RNA species named "meiRNA". Pat1 kinase phosphorylates Mei2p on two positions and downregulates its activity. Pat1 kinase undergoes inactivation under meiotic conditions, as a result of the production of a tethering pseudosubstrate Mei3p, and accumulation of the unphosphorylated form of Mei2p commits cells to meiosis. However, the mechanism of how phosphorylation of Mei2p suppresses its activity to induce meiosis remains largely unknown. Here we show that S. pombe Rad24p, a 14-3-3 protein, functions as a negative factor for meiosis by antagonizing the function of meiRNA to promote the formation of a nuclear Mei2p dot. Rad24p binds preferentially to Mei2p phosphorylated by Pat1 kinase. It inhibits association of meiRNA to the phosphorylated form of Mei2p but not to the unphosphorylated form in vitro. We speculate that Rad24p, bound tightly to the residues phosphorylated by Pat1 kinase, may mask the RNA recognition motifs on Mei2p. This model will explain, at least partly, why phosphorylation by Pat1 kinase inhibits the meiosis-inducing activity of Mei2p.
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Affiliation(s)
- Masamitsu Sato
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Hongo, Japan
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22
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Current awareness on yeast. Yeast 2001; 18:1357-64. [PMID: 11571760 DOI: 10.1002/yea.690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Kitamura K, Katayama S, Dhut S, Sato M, Watanabe Y, Yamamoto M, Toda T. Phosphorylation of Mei2 and Ste11 by Pat1 kinase inhibits sexual differentiation via ubiquitin proteolysis and 14-3-3 protein in fission yeast. Dev Cell 2001; 1:389-99. [PMID: 11702950 DOI: 10.1016/s1534-5807(01)00037-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Fission yeast Pat1 kinase inhibits sexual differentiation by phosphorylating the meiotic inducer Mei2 and the transcription factor Ste11. Here, we show how Pat1 downregulates these proteins. Mei2 is degraded via a ubiquitin-proteasome pathway in a phosphorylation-dependent fashion. The E2 Ubc2 and the E3 Ubr1 are required for this proteolysis. In addition, Pat1 negatively regulates Ste11 via Rad24/14-3-3, thereby repressing mei2+ transcription. The Pat1 phosphorylation sites of Ste11 match the consensus recognition sequence for 14-3-3. Rad24 binds preferentially to phosphorylated Ste11, and this binding results in inhibition of the transcriptional activation capacity of Ste11. Overall, therefore, these results show that Pat1 coordinates concerted molecular mechanisms that govern the sexual differentiation developmental decision.
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Affiliation(s)
- K Kitamura
- Laboratory of Cell Regulation, Imperial Cancer Research Fund, United Kingdom.
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