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Sun L, Sun G, Shi C, Sun D. Transcriptome analysis reveals new microRNAs-mediated pathway involved in anther development in male sterile wheat. BMC Genomics 2018; 19:333. [PMID: 29739311 PMCID: PMC5941544 DOI: 10.1186/s12864-018-4727-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/25/2018] [Indexed: 11/16/2022] Open
Abstract
Background 337S is a novel bi-pole-photo-thermo-sensitive genic male sterile line in wheat, and sensitive to both long day length/high temperature and short day length/low temperature condition. Although the regulatory function of MicroRNAs (miRNAs) in reproductive development has been increasingly studied, their roles in pre-meiotic and meiotic cells formation of plants have not been clearly explored. Here, we explored the roles of miRNAs in regulating male sterility of 337S at short day length/low temperature condition. Results Small RNA sequencing and degradome analyses were employed to identify miRNAs and their targets in the 337S whose meiotic cells collapsed rapidly during male meiotic prophase, resulting in failure of meiosis at SL condition. A total of 102 unique miRNAs were detected. Noticeably, the largest miRNA family was MiR1122. The target CCR4-associated factor 1 (CAF1) of miR2275, a subunit of the Carbon Catabolite Repressed 4-Negative on TATA-less (CCR4-NOT) complex, contributes to the process of early meiosis, and was first identified here. Further studies showed that the expression of several pivotal anther-related miRNAs was altered in 337S at SL condition, especially tae-miR1127a, which may be related to male sterility of 337S. Here, we also identified a new member of SWI/SNF factors SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A, member 3-like 3 (SMARCA3L3) targeted by tae-miR1127a, whose function might be involved in faithful progression of meiosis in male reproductive cells. Conclusion The miRNA-target interactions of tae-miR2275-CAF1 and tae-miR1127a-SMARCA3L3 might be involved in regulating male fertility in 337S. Our results also implied that multiple roles for SMARCA3L3 and CAF1 in DNA repair and transcriptional regulation jointly orchestrated a tight and orderly system for maintaining chromatin and genome integrity during meiosis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4727-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Longqing Sun
- College of plant science & technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
| | - Chenxia Shi
- College of plant science & technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dongfa Sun
- College of plant science & technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. .,Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, 434025, Hubei, China.
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102
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Deng P, Muhammad S, Cao M, Wu L. Biogenesis and regulatory hierarchy of phased small interfering RNAs in plants. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:965-975. [PMID: 29327403 PMCID: PMC5902766 DOI: 10.1111/pbi.12882] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/28/2017] [Accepted: 01/03/2018] [Indexed: 05/02/2023]
Abstract
Several varieties of small RNAs including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are generated in plants to regulate development, genome stability and response to adverse environments. Phased siRNA (phasiRNA) is a type of secondary siRNA that is processed from a miRNA-mediated cleavage of RNA transcripts, increasing silencing efficiency or simultaneously suppressing multiple target genes. Trans-acting siRNAs (ta-siRNAs) are a particular class of phasiRNA produced from noncoding transcripts that silence targets in trans. It was originally thought that 'one-hit' and 'two-hit' models were essential for processing distinct TAS precursors; however, a single hit event was recently shown to be sufficient at triggering all types of ta-siRNAs. This review discusses the findings about biogenesis, targeting modes and regulatory networks of plant ta-siRNAs. We also summarize recent advances in the generation of other phasiRNAs and their possible biological benefits to plants.
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Affiliation(s)
- Pingchuan Deng
- Department of AgronomyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Sajid Muhammad
- Department of AgronomyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Min Cao
- Department of AgronomyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Liang Wu
- Department of AgronomyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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Abstract
Meiosis halves diploid chromosome numbers to haploid levels that are essential for sexual reproduction in most eukaryotes. Meiotic recombination ensures the formation of bivalents between homologous chromosomes (homologs) and their subsequent proper segregation. It also results in genetic diversity among progeny that influences evolutionary responses to selection. Moreover, crop breeding depends upon the action of meiotic recombination to rearrange elite traits between parental chromosomes. An understanding of the molecular mechanisms that drive meiotic recombination is important for both fundamental research and practical applications. This review emphasizes advances made during the past 5 years, primarily in Arabidopsis and rice, by summarizing newly characterized genes and proteins and examining the regulatory mechanisms that modulate their action.
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Affiliation(s)
- Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China;
| | - Gregory P Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA;
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-3280, USA
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105
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Ren L, Tang D, Zhao T, Zhang F, Liu C, Xue Z, Shi W, Du G, Shen Y, Li Y, Cheng Z. OsSPL regulates meiotic fate acquisition in rice. THE NEW PHYTOLOGIST 2018; 218:789-803. [PMID: 29479720 DOI: 10.1111/nph.15017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/28/2017] [Indexed: 05/20/2023]
Abstract
In angiosperms, the key step in sexual reproduction is successful acquisition of meiotic fate. However, the molecular mechanism determining meiotic fate remains largely unknown. Here, we report that OsSPOROCYTELESS (OsSPL) is critical for meiotic entry in rice (Oryza sativa). We performed a large-scale genetic screen of rice sterile mutants aimed to identify genes regulating meiotic entry and identified OsSPL using map-based cloning. We showed that meiosis-specific callose deposition, chromatin organization, and centromere-specific histone H3 loading were altered in the cells corresponding to pollen mother cells in Osspl anthers. Global transcriptome analysis showed that the enriched differentially expressed genes in Osspl were mainly related to redox status, meiotic process, and parietal cell development. OsSPL might form homodimers and interact with TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factor OsTCP5 via the SPL dimerization and TCP interaction domain. OsSPL also interacts with TPL (TOPLESS) corepressors, OsTPL2 and OsTPL3, via the EAR motif. Our results suggest that the OsSPL-mediated signaling pathway plays a crucial role in rice meiotic entry, which appears to be a conserved regulatory mechanism for meiotic fate acquisition in angiosperms.
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Affiliation(s)
- Lijun Ren
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tingting Zhao
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fanfan Zhang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changzhen Liu
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhihui Xue
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenqing Shi
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guijie Du
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Shen
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
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106
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Nonomura KI. Small RNA pathways responsible for non-cell-autonomous regulation of plant reproduction. PLANT REPRODUCTION 2018; 31:21-29. [PMID: 29350289 DOI: 10.1007/s00497-018-0321-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/04/2018] [Indexed: 05/21/2023]
Abstract
In angiosperms, germline precursors and germ cells are always attached to or engulfed within somatic companion cells until just before fertilization. This is because sperm and egg cells develop as part of the multicellular gametophyte. Thus, the non-cell-autonomous regulation by somatic companions plays important roles in efficient reproduction, in addition to the cell-autonomous regulation. Epigenetic silencing of transposable elements is one of the central events by which the germline transmits the error-free genome to the next generation. This review focuses on small RNA-mediated epigenetic regulation of meiosis, spore formation and pollen development. Besides microRNA (miRNA) and small interfering RNA (siRNA), animals express PIWI-interacting RNA (piRNA), a germline-specific class of small RNAs. Plants lack piRNA-like RNAs and, instead, express unique classes of small RNAs: trans-acting siRNA (tasiRNA) and phased secondary siRNA (phasiRNA). Especially in grass species, 21- and 24-nucleotide phasiRNAs are abundant in anthers during premeiosis and meiosis. This review also describes recent progress in reproductive phasiRNA research.
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Affiliation(s)
- Ken-Ichi Nonomura
- Experimental Farm, National Institute of Genetics, Yata 1111, Shizuoka, 411-8540, Japan.
- Department of Life Science, Graduate University for Advanced Studies/SOKENDAI, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
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Ono S, Liu H, Tsuda K, Fukai E, Tanaka K, Sasaki T, Nonomura KI. EAT1 transcription factor, a non-cell-autonomous regulator of pollen production, activates meiotic small RNA biogenesis in rice anther tapetum. PLoS Genet 2018; 14:e1007238. [PMID: 29432414 PMCID: PMC5825165 DOI: 10.1371/journal.pgen.1007238] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 02/23/2018] [Accepted: 02/01/2018] [Indexed: 11/18/2022] Open
Abstract
The 24-nucleotides (nt) phased secondary small interfering RNA (phasiRNA) is a unique class of plant small RNAs abundantly expressed in monocot anthers at early meiosis. Previously, 44 intergenic regions were identified as the loci for longer precursor RNAs of 24-nt phasiRNAs (24-PHASs) in the rice genome. However, the regulatory mechanism that determines spatiotemporal expression of these RNAs has remained elusive. ETERNAL TAPETUM1 (EAT1) is a basic-helix-loop-helix (bHLH) transcription factor indispensable for induction of programmed cell death (PCD) in postmeiotic anther tapetum, the somatic nursery for pollen production. In this study, EAT1-dependent non-cell-autonomous regulation of male meiosis was evidenced from microscopic observation of the eat1 mutant, in which meiosis with aberrantly decondensed chromosomes was retarded but accomplished somehow, eventually resulting in abortive microspores due to an aberrant tapetal PCD. EAT1 protein accumulated in tapetal-cell nuclei at early meiosis and postmeiotic microspore stages. Meiotic EAT1 promoted transcription of 24-PHAS RNAs at 101 loci, and importantly, also activated DICER-LIKE5 (DCL5, previous DCL3b in rice) mRNA transcription that is required for processing of double-stranded 24-PHASs into 24-nt lengths. From the results of the chromatin-immunoprecipitation and transient expression analyses, another tapetum-expressing bHLH protein, TDR INTERACTING PROTEIN2 (TIP2), was suggested to be involved in meiotic small-RNA biogenesis. The transient assay also demonstrated that UNDEVELOPED TAPETUM1 (UDT1)/bHLH164 is a potential interacting partner of both EAT1 and TIP2 during early meiosis. This study indicates that EAT1 is one of key regulators triggering meiotic phasiRNA biogenesis in anther tapetum, and that other bHLH proteins, TIP2 and UDT1, also play some important roles in this process. Spatiotemporal expression control of these bHLH proteins is a clue to orchestrate precise meiosis progression and subsequent pollen production non-cell-autonomously.
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Affiliation(s)
- Seijiro Ono
- Experimental Farm, National Institute of Genetics, Yata, Mishima, Shizuoka, Japan
| | - Hua Liu
- Experimental Farm, National Institute of Genetics, Yata, Mishima, Shizuoka, Japan
| | - Katsutoshi Tsuda
- Experimental Farm, National Institute of Genetics, Yata, Mishima, Shizuoka, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Yata, Mishima, Shizuoka, Japan
| | - Eigo Fukai
- Graduate School of Science and Technology, Niigata University, Ikarashi, Nishi-ku, Niigata, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, Japan
| | - Takuji Sasaki
- NODAI Research Institute, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, Japan
| | - Ken-Ichi Nonomura
- Experimental Farm, National Institute of Genetics, Yata, Mishima, Shizuoka, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Yata, Mishima, Shizuoka, Japan
- * E-mail:
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108
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Yuan TL, Huang WJ, He J, Zhang D, Tang WH. Stage-Specific Gene Profiling of Germinal Cells Helps Delineate the Mitosis/Meiosis Transition. PLANT PHYSIOLOGY 2018; 176:1610-1626. [PMID: 29187566 PMCID: PMC5813559 DOI: 10.1104/pp.17.01483] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/26/2017] [Indexed: 05/11/2023]
Abstract
In flowering plants, germ lines are induced from somatic meristems within reproductive organs. Within anthers, germinal cell initials first undergo several rounds of mitotic proliferation before synchronously entering meiosis. Our understanding of the progression and the molecular basis of this mitosis to meiosis transition is still limited. Taking advantage of the correlation between anther length and premeiotic germinal cell development in maize (Zea mays), we studied the transcriptome dynamics of germinal cells at three sequential stages, mitotic archesporial cells, enlarging pollen mother cells at the premeiosis interphase, and pollen mother cells at the early prophase of meiosis, using laser microdissection-based expression profiling. Our analysis showed that cells undergoing the mitosis-meiosis switch exhibit robust transcriptional changes. The three stages are distinguished by the expression of genes encoding transcription factor subsets, meiotic chromosome recombination proteins, and distinct E3 ubiquitin ligases, respectively. The transcription level of genes encoding protein turnover machinery was significantly higher in these three stages of germinal cells than in mature pollen, parenchyma cells, or seedlings. Our experimental results further indicate that many meiotic genes are not only transcribed, but also translated prior to meiosis. We suggest that the enlarging pollen mother cells stage represents a crucial turning point from mitosis to meiosis for developing germinal cells.
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Affiliation(s)
- Ting-Lu Yuan
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wei-Jie Huang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Juan He
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Dong Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wei-Hua Tang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Osman K, Yang J, Roitinger E, Lambing C, Heckmann S, Howell E, Cuacos M, Imre R, Dürnberger G, Mechtler K, Armstrong S, Franklin FCH. Affinity proteomics reveals extensive phosphorylation of the Brassica chromosome axis protein ASY1 and a network of associated proteins at prophase I of meiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:17-33. [PMID: 29078019 PMCID: PMC5767750 DOI: 10.1111/tpj.13752] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/10/2017] [Accepted: 10/17/2017] [Indexed: 05/18/2023]
Abstract
During meiosis, the formation of crossovers (COs) generates genetic variation and provides physical links that are essential for accurate chromosome segregation. COs occur in the context of a proteinaceous chromosome axis. The transcriptomes and proteomes of anthers and meiocytes comprise several thousand genes and proteins, but because of the level of complexity relatively few have been functionally characterized. Our understanding of the physical and functional interactions between meiotic proteins is also limited. Here we use affinity proteomics to analyse the proteins that are associated with the meiotic chromosome axis protein, ASY1, in Brassica oleracea anthers and meiocytes. We show that during prophase I ASY1 and its interacting partner, ASY3, are extensively phosphorylated, and we precisely assign phosphorylation sites. We identify 589 proteins that co-immunoprecipitate with ASY1. These correspond to 492 Arabidopsis orthologues, over 90% of which form a coherent protein-protein interaction (PPI) network containing known and candidate meiotic proteins, including proteins more usually associated with other cellular processes such as DNA replication and proteolysis. Mutant analysis confirms that affinity proteomics is a viable strategy for revealing previously unknown meiotic proteins, and we show how the PPI network can be used to prioritise candidates for analysis. Finally, we identify another axis-associated protein with a role in meiotic recombination. Data are available via ProteomeXchange with identifier PXD006042.
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Affiliation(s)
- Kim Osman
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Jianhua Yang
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Faculty of Engineering and ComputingCoventry UniversityCoventryCV1 5FBUK
| | | | - Christophe Lambing
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Department of Plant SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EAUK
| | - Stefan Heckmann
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)OT Gatersleben, Corrensstrasse 3D‐06466Stadt SeelandGermany
| | - Elaine Howell
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Maria Cuacos
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
- Present address:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)OT Gatersleben, Corrensstrasse 3D‐06466Stadt SeelandGermany
| | | | - Gerhard Dürnberger
- IMP‐IMBA1030ViennaAustria
- Gregor Mendel Institute of Molecular Plant BiologyDr. Bohr‐Gasse 31030ViennaAustria
| | | | - Susan Armstrong
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
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Lambing C, Heckmann S. Tackling Plant Meiosis: From Model Research to Crop Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:829. [PMID: 29971082 PMCID: PMC6018109 DOI: 10.3389/fpls.2018.00829] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/28/2018] [Indexed: 05/04/2023]
Abstract
Genetic engineering and traditional plant breeding, which harnesses the natural genetic variation that arises during meiosis, will have key roles to improve crop varieties and thus deliver Food Security in the future. Meiosis, a specialized cell division producing haploid gametes to maintain somatic diploidy following their fusion, assures genetic variation by regulated genetic exchange through homologous recombination. However, meiotic recombination events are restricted in their total number and their distribution along chromosomes limiting allelic variations in breeding programs. Thus, modifying the number and distribution of meiotic recombination events has great potential to improve and accelerate plant breeding. In recent years much progress has been made in understanding meiotic progression and recombination in plants. Many genes and factors involved in these processes have been identified primarily in Arabidopsis thaliana but also more recently in crops such as Brassica, rice, barley, maize, or wheat. These advances put researchers in the position to translate acquired knowledge to various crops likely improving and accelerating breeding programs. However, although fundamental aspects of meiotic progression and recombination are conserved between species, differences in genome size and organization (due to repetitive DNA content and ploidy level) exist, particularly among plants, that likely account for differences in meiotic progression and recombination patterns found between species. Thus, tools and approaches are needed to better understand differences and similarities in meiotic progression and recombination among plants, to study fundamental aspects of meiosis in a variety of plants including crops and non-model species, and to transfer knowledge into crop species. In this article, we provide an overview of tools and approaches available to study plant meiosis, highlight new techniques, give examples of areas of future research and review distinct aspects of meiosis in non-model species.
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Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Christophe Lambing, Stefan Heckmann,
| | - Stefan Heckmann
- Independent Research Group Meiosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- *Correspondence: Christophe Lambing, Stefan Heckmann,
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111
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KLU suppresses megasporocyte cell fate through SWR1-mediated activation of WRKY28 expression in Arabidopsis. Proc Natl Acad Sci U S A 2017; 115:E526-E535. [PMID: 29288215 DOI: 10.1073/pnas.1716054115] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Germ-line specification is essential for sexual reproduction. In the ovules of most flowering plants, only a single hypodermal cell enlarges and differentiates into a megaspore mother cell (MMC), the founder cell of the female germ-line lineage. The molecular mechanisms restricting MMC specification to a single cell remain elusive. We show that the Arabidopsis transcription factor WRKY28 is exclusively expressed in hypodermal somatic cells surrounding the MMC and is required to repress these cells from acquiring MMC-like cell identity. In this process, the SWR1 chromatin remodeling complex mediates the incorporation of the histone variant H2A.Z at the WRKY28 locus. Moreover, the cytochrome P450 gene KLU, expressed in inner integument primordia, non-cell-autonomously promotes WRKY28 expression through H2A.Z deposition at WRKY28. Taken together, our findings show how somatic cells in ovule primordia cooperatively use chromatin remodeling to restrict germ-line cell specification to a single cell.
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112
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Wu J, Chen L, Shahid MQ, Chen M, Dong Q, Li J, Xu X, Liu X. Pervasive interactions of Sa and Sb loci cause high pollen sterility and abrupt changes in gene expression during meiosis that could be overcome by double neutral genes in autotetraploid rice. RICE (NEW YORK, N.Y.) 2017; 10:49. [PMID: 29197985 PMCID: PMC5712294 DOI: 10.1186/s12284-017-0188-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/22/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Intersubspecific autotetraploid rice hybrids possess high hybrid vigor; however, low pollen fertility is a critical hindrance in its commercial utilization. Our previous study demonstrated that polyploidy could increase the multi-loci interaction and cause high pollen abortion in autotetraploid rice hybrids. However, there is little known about the critical role of pollen sterility locus or loci in the intersubspecific hybrids. We developed autotetraploid rice hybrids harboring heterozygous genotypes (S i S i S j S j ) at different pollen sterility loci by using the near isogenic lines of Taichung65-4×. Moreover, autotetraploid lines carrying double neutral genes, Sa n and Sb n , were used to assess their effect on fertility restoration. RESULTS Cytological studies showed that the deleterious genetic interactions at Sa and Sb pollen sterility loci resulted in higher pollen sterility (76.83%) and abnormal chromosome behavior (24.59%) at metaphase I of meiosis in autotetraploid rice hybrids. Transcriptome analysis revealed 1092 differentially expressed genes (DEG) in a hybrid with the pervasive interactions at Sa and Sb pollen sterility loci, and most of the genes (about 83%) exhibited down regulation. Of the DEG, 60 were associated with transcription regulation and 18 genes were annotated as meiosis-related genes. Analysis on the hybrids developed by using autotetraploid rice harboring double neutral genes, Sa n and Sb n , revealed normal pollen fertility, and transcriptome analysis showed non-significant difference in number of DEG among different hybrids. CONCLUSIONS Our finding revealed that pervasive interactions at Sa and Sb pollen sterility loci cause high sterility in the autotetraploid hybrids that lead to the down-regulation of important meiosis-related genes and transcription regulation factors. Moreover, we also found that the hybrids sterility could be overcome by double neutral genes, Sa n and Sb n , in autotetraploid rice hybrids. The present study provided a strong evidence for the utilization of heterosis in autotetraploid rice hybrids.
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Affiliation(s)
- Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Lin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Minyi Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Qinglei Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Jirui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Xiaosong Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
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D'Ario M, Griffiths-Jones S, Kim M. Small RNAs: Big Impact on Plant Development. TRENDS IN PLANT SCIENCE 2017; 22:1056-1068. [PMID: 29032035 DOI: 10.1016/j.tplants.2017.09.009] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 05/19/2023]
Abstract
While the role of proteins in determining cell identity has been extensively studied, the contribution of small noncoding RNA molecules such as miRNAs and siRNAs has been also recognised. miRNAs bind to complementary sites in target mRNA molecules to trigger the degradation or translational inhibition of those targets. Recent studies have revealed that miRNAs play pivotal roles in key developmental processes such as patterning of the embryo, meristem, leaf, and flower. Furthermore, these miRNAs have been recruited throughout plant evolution into pathways that create diverse plant organ forms and shapes. This review focuses on the roles of miRNAs in establishing plant cell identity during key plant development processes and creating morphological diversity during plant evolution.
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Affiliation(s)
- Marco D'Ario
- Faculty of Biology, Medicine, and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Sam Griffiths-Jones
- Faculty of Biology, Medicine, and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
| | - Minsung Kim
- Faculty of Biology, Medicine, and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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Singh SK, Kumar V, Srinivasan R, Ahuja PS, Bhat SR, Sreenivasulu Y. The TRAF Mediated Gametogenesis Progression ( TRAMGaP) Gene Is Required for Megaspore Mother Cell Specification and Gametophyte Development. PLANT PHYSIOLOGY 2017; 175:1220-1237. [PMID: 28939625 PMCID: PMC5664457 DOI: 10.1104/pp.17.00275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/17/2017] [Indexed: 05/03/2023]
Abstract
In plants, the role of TRAF-like proteins with meprin and the TRAF homology (MATH) domain is far from clear. In animals, these proteins serve as adapter molecules to mediate signal transduction from Tumor Necrosis Factor Receptor to downstream effector molecules. A seed-sterile mutant with a disrupted TRAF-like gene (At5g26290) exhibiting aberrant gametogenesis led us to investigate the developmental role of this gene in Arabidopsis (Arabidopsis thaliana). The mutation was semidominant and resulted in pleiotropic phenotypes with such features as short siliques with fewer ovules, pollen and seed sterility, altered Megaspore Mother Cell (MMC) specification, and delayed programmed cell death in megaspores and the tapetum, features that overlapped those in other well-characterized mutants. Seed sterility and reduced transmission frequency of the mutant alleles pointed to a dual role, sporophytic and gametophytic, for the gene on the male side. The mutant also showed altered expression of various genes involved in such cellular and developmental pathways as regulation of transcription, biosynthesis and transport of lipids, hormone-mediated signaling, and gametophyte development. The diverse phenotypes of the mutant and the altered expression of key genes related to gametophyte and seed development could be explained based on the functional similarly between At5g26290 and MATH-BTB domain proteins that modulate gene expression through the ubiquitin-mediated proteasome system. These results show a novel link between a TRAF-like gene and reproductive development in plants.
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Affiliation(s)
- Sunil Kumar Singh
- Biotechnology Division, Council of Scientific and Industrial Research CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Vajinder Kumar
- Indian Council of Agricultural Research ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | - Ramamurthy Srinivasan
- Indian Council of Agricultural Research ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | - Paramvir Singh Ahuja
- Biotechnology Division, Council of Scientific and Industrial Research CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Shripad Ramchandra Bhat
- Indian Council of Agricultural Research ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India
| | - Yelam Sreenivasulu
- Biotechnology Division, Council of Scientific and Industrial Research CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
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115
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Yu Y, Zhou Y, Zhang Y, Chen Y. Grass phasiRNAs and male fertility. SCIENCE CHINA-LIFE SCIENCES 2017; 61:148-154. [PMID: 29052095 DOI: 10.1007/s11427-017-9166-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 07/25/2017] [Indexed: 01/01/2023]
Abstract
Recent studies have indicated that a special type of small noncoding RNAs, phased small-interfering RNAs (phasiRNAs) play crucial roles in many cellular processes of plant development. PhasiRNAs are generated from long RNA precursors at intervals of 21 or 24 nt in plants, and they are produced from both protein-coding gene and long noncoding RNA genes. Different from those in eudicots, grass phasiRNAs include a special class of small RNAs that are specifically expressed in reproductive organs. These grass phasiRNAs are associated with gametogenesis, especially with anther development and male fertility. In this review, we summarized current knowledge on these small noncoding RNAs in male germ cells and their possible biological functions and mechanisms in grass species.
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Affiliation(s)
- Yang Yu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yanfei Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuchan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yueqin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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116
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117
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Oliver C, Pradillo M, Jover-Gil S, Cuñado N, Ponce MR, Santos JL. Loss of function of Arabidopsis microRNA-machinery genes impairs fertility, and has effects on homologous recombination and meiotic chromatin dynamics. Sci Rep 2017; 7:9280. [PMID: 28839139 PMCID: PMC5571030 DOI: 10.1038/s41598-017-07702-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/30/2017] [Indexed: 02/03/2023] Open
Abstract
MicroRNAs (miRNAs) are ~22-nt single-stranded noncoding RNAs with regulatory roles in a wide range of cellular functions by repressing eukaryotic gene expression at a post-transcriptional level. Here, we analyzed the effects on meiosis and fertility of hypomorphic or null alleles of the HYL1, HEN1, DCL1, HST and AGO1 genes, which encode miRNA-machinery components in Arabidopsis. Reduced pollen and megaspore mother cell number and fertility were shown by the mutants analyzed. These mutants also exhibited a relaxed chromatin conformation in male meiocytes at the first meiotic division, and increased chiasma frequency, which is likely to be due to increased levels of mRNAs from key genes involved in homologous recombination. The hen1-13 mutant was found to be hypersensitive to gamma irradiation, which mainly causes double-strand breaks susceptible to be repaired by homologous recombination. Our findings uncover a role for miRNA-machinery components in Arabidopsis meiosis, as well as in the repression of key genes required for homologous recombination. These genes seem to be indirect miRNA targets.
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Affiliation(s)
- Cecilia Oliver
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, 28040, Madrid, Spain.,Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 34396, Montpellier, cedex 05, France
| | - Mónica Pradillo
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Sara Jover-Gil
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Nieves Cuñado
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain.
| | - Juan Luis Santos
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, 28040, Madrid, Spain.
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Odokonyero D, Mendoza MR, Moffett P, Scholthof HB. Tobacco rattle virus (TRV)-Mediated Silencing of Nicotiana benthamiana ARGONAUTES (NbAGOs) Reveals New Antiviral Candidates and Dominant Effects of TRV-NbAGO1. PHYTOPATHOLOGY 2017; 107:977-987. [PMID: 28636437 DOI: 10.1094/phyto-02-17-0049-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The objective of this study was to determine the contribution of different ARGONAUTE proteins in Nicotiana benthamiana (NbAGOs) to the defense against silencing sensitive GFP-expressing viral constructs based on Tomato bushy stunt virus (TBSV) (Tombusvirus), Sunn-hemp mosaic virus (Tobamovirus), and Foxtail mosaic virus (Potexvirus). Upon Tobacco rattle virus (TRV)-mediated down-regulation of NbAGO1, 4, 5, or 6, no effects were noted on susceptibility to any virus construct, whereas knockdown of NbAGO2 specifically prevented silencing of P19-defective TBSV (TGdP19). Down-regulation of a new gene referred to as NbAGO5L showed some reduced silencing for TGdP19 but not for the other two virus constructs, whereas silencing of NbAGO7 gave rise to a subtle increase in susceptibility to all three viruses. Co-infiltrating different TRV-NbAGO constructs simultaneously did not enhance virus susceptibility. However, an unexpected finding was that whenever the TRV-NbAGO1 construct was present, this compromised silencing of genes targeted by co-infiltrated constructs, as shown upon co-infiltration of TRV-NbAGO1 with either TRV-NbAGO2 or TRV-Sul (targeting Magnesium chelatase I). Only after a prolonged period (approximately 2 months) did TRV-Sul-mediated systemic bleaching occur in these co-infected plants, suggesting that TRV-NbAGO1 hinders the silencing ability of other TRV-NbAGO constructs. In conclusion, this study revealed new antiviral NbAGOs and dominant effects of silencing NbAGO1.
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Affiliation(s)
- Denis Odokonyero
- First, second, and fourth authors: Department of Plant Pathology and Microbiology, Texas A&M University, College Station; and third author: Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Maria R Mendoza
- First, second, and fourth authors: Department of Plant Pathology and Microbiology, Texas A&M University, College Station; and third author: Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Peter Moffett
- First, second, and fourth authors: Department of Plant Pathology and Microbiology, Texas A&M University, College Station; and third author: Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Herman B Scholthof
- First, second, and fourth authors: Department of Plant Pathology and Microbiology, Texas A&M University, College Station; and third author: Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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119
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Sun W, Hui Xu X, Lu X, Xie L, Bai B, Zheng C, Sun H, He Y, Xie XZ. The Rice Phytochrome Genes, PHYA and PHYB, Have Synergistic Effects on Anther Development and Pollen Viability. Sci Rep 2017; 7:6439. [PMID: 28743949 PMCID: PMC5527001 DOI: 10.1038/s41598-017-06909-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/20/2017] [Indexed: 12/21/2022] Open
Abstract
Phytochromes are the main plant photoreceptors regulating multiple developmental processes. However, the regulatory network of phytochrome-mediated plant reproduction has remained largely unexplored. There are three phytochromes in rice, phyA, phyB and phyC. No changes in fertility are observed in the single mutants, whereas the seed-setting rate of the phyA phyB double mutant is significantly reduced. Histological and cytological analyses showed that the reduced fertility of the phyA phyB mutant was due to defects in both anther and pollen development. The four anther lobes in the phyA phyB mutant were developed at different stages with fewer pollen grains, most of which were aborted. At the mature stage, more than one lobe in the double mutant was just consisted of several cell layers. To identify genes involved in phytochrome-mediated anther development, anther transcriptomes of phyA, phyB and phyA phyB mutants were compared to that of wild-type rice respectively. Analysis of 2,241 double-mutant-specific differentially expressed transcripts revealed that the metabolic profiles, especially carbohydrate metabolism, were altered greatly, and heat-shock responses were activated in the double mutant. This study firstly provides valuable insight into the complex regulatory networks underlying phytochrome-mediated anther and pollen development in plants, and offers novel clues for hybrid rice breeding.
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Affiliation(s)
- Wei Sun
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250100, China
| | - Xiao Hui Xu
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Shandong Key Laboratory of Plant Virology, Ji'nan, 250100, China
| | - Xingbo Lu
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Shandong Key Laboratory of Plant Virology, Ji'nan, 250100, China
| | - Lixia Xie
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250100, China
| | - Bo Bai
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250100, China
| | - Chongke Zheng
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250100, China
| | - Hongwei Sun
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Shandong Key Laboratory of Plant Virology, Ji'nan, 250100, China
| | - Yanan He
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250100, China
| | - Xian-Zhi Xie
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250100, China.
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120
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Genetic Subtraction Profiling Identifies Candidate miRNAs Involved in Rice Female Gametophyte Abortion. G3-GENES GENOMES GENETICS 2017; 7:2281-2293. [PMID: 28526728 PMCID: PMC5499135 DOI: 10.1534/g3.117.040808] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The female gametophyte is an important participant in the sexual reproduction of plants. The molecular mechanism of its development has received much attention in recent years. As important regulators of gene expression, miRNAs have been certified to play a significant role in many biological processes of plants, including sexual reproduction. In this study, to investigate the potential regulatory effects of miRNAs on rice female gametophyte abortion, we used the high-throughput sequencing method to compare the miRNA transcriptome in ovules of a high frequency female-sterile line (fsv1) and a rice wild-type line (Gui 99) during ovule development. As a result, 522 known miRNAs and 295 novel miRNAs were expressed in the developing ovule of rice, while 100 known miRNAs were significantly differentially expressed between these two rice lines during ovule development. Combining with gene expression information, a total of 627 coherent target genes of these differential expressed known miRNAs between fsv1 and Gui 99 were identified. The functional analyses of these coherent target genes revealed that the coherent target genes of differential expressed known miRNAs between the two rice lines are involved in many biological pathways, such as protein degradation, auxin signal transduction, and transcription factor regulation. These results provide us with important clues to investigate the regulatory roles of miRNAs in rice female gametophyte abortion.
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121
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Su Z, Zhao L, Zhao Y, Li S, Won S, Cai H, Wang L, Li Z, Chen P, Qin Y, Chen X. The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module. Curr Biol 2017; 27:1597-1609.e2. [PMID: 28552357 DOI: 10.1016/j.cub.2017.05.021] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 04/12/2017] [Accepted: 05/05/2017] [Indexed: 12/21/2022]
Abstract
In most sexually reproducing plants, a single somatic, sub-epidermal cell in an ovule is selected to differentiate into a megaspore mother cell, which is committed to giving rise to the female germline. However, it remains unclear how intercellular signaling among somatic cells results in only one cell in the sub-epidermal layer differentiating into the megaspore mother cell. Here we uncovered a role of the THO complex in restricting the megaspore mother cell fate to a single cell. Mutations in TEX1, HPR1, and THO6, components of the THO/TREX complex, led to the formation of multiple megaspore mother cells, which were able to initiate gametogenesis. We demonstrated that TEX1 repressed the megaspore mother cell fate by promoting the biogenesis of TAS3-derived trans-acting small interfering RNA (ta-siRNA), which represses ARF3 expression. The TEX1 protein was present in epidermal cells, but not in the germline, and, through TAS3-derived ta-siRNA, restricted ARF3 expression to the medio domain of ovule primordia. Expansion of ARF3 expression into lateral epidermal cells in a TAS3 ta-siRNA-insensitive mutant led to the formation of supernumerary megaspore mother cells, suggesting that TEX1- and TAS3-mediated restriction of ARF3 expression limits excessive megaspore mother cell formation non-cell-autonomously. Our findings reveal the role of a small-RNA pathway in the regulation of female germline specification in Arabidopsis.
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Affiliation(s)
- Zhenxia Su
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Lab of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, 92521, USA
| | - Lihua Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Lab of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, 92521, USA
| | - Shaofang Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, 92521, USA
| | - SoYoun Won
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, 92521, USA
| | - Hanyang Cai
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Lab of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Lulu Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Lab of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Zhenfang Li
- Crop Science College, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Piaojuan Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Lab of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Lab of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China.
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, 92521, USA; Howard Hughes Medical Institute, Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, 92521, USA.
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Tang Q, Zang G, Cheng C, Luan M, Dai Z, Xu Y, Yang Z, Zhao L, Su J. Diplosporous development in Boehmeria tricuspis: Insights from de novo transcriptome assembly and comprehensive expression profiling. Sci Rep 2017; 7:46043. [PMID: 28382950 PMCID: PMC5382578 DOI: 10.1038/srep46043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/07/2017] [Indexed: 01/05/2023] Open
Abstract
Boehmeria tricuspis includes sexually reproducing diploid and apomictic triploid individuals. Previously, we established that triploid B. tricuspis reproduces through obligate diplospory. To understand the molecular basis of apomictic development in B. tricuspis, we sequenced and compared transcriptomic profiles of the flowers of sexual and apomictic plants at four key developmental stages. A total of 283,341 unique transcripts were obtained from 1,463 million high-quality paired-end reads. In total, 18,899 unigenes were differentially expressed between the reproductive types at the four stages. By classifying the transcripts into gene ontology categories of differentially expressed genes, we showed that differential plant hormone signal transduction, cell cycle regulation, and transcription factor regulation are possibly involved in apomictic development and/or a polyploidization response in B. tricuspis. Furthermore, we suggest that specific gene families are possibly related to apomixis and might have important effects on diplosporous floral development. These results make a notable contribution to our understanding of the molecular basis of diplosporous development in B. tricuspis.
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Affiliation(s)
- Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Gonggu Zang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Lining Zhao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
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123
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Martinez G, Köhler C. Role of small RNAs in epigenetic reprogramming during plant sexual reproduction. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:22-28. [PMID: 28088028 DOI: 10.1016/j.pbi.2016.12.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/29/2016] [Indexed: 05/07/2023]
Abstract
Sexual reproduction, the formation of a new individual from specialized reproductive cells after fertilization, involves the precise orchestration of different developmental and genomic processes. These processes are to a large extent governed by small RNAs (sRNAs) that either belong to the class of micro RNAs (miRNAs) or small-interfering RNAs (siRNAs). The latter are derived from transposable elements (TEs) and involved in genome defense and transgenerational inheritance of heterochromatin identity, ensuring genome stability. Remarkably, male and female gametophytes employ sRNAs to ensure reproductive success, but the underlying processes of their formation and action differ. Here, we review current advances in the field concerning the roles of sRNAs during flowering plant (angiosperm) reproduction and pinpoint where further research is required to solve open questions.
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Affiliation(s)
- German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
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Zhou L, Han J, Chen Y, Wang Y, Liu YG. Bivalent Formation 1, a plant-conserved gene, encodes an OmpH/coiled-coil motif-containing protein required for meiotic recombination in rice. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2163-2174. [PMID: 28369589 PMCID: PMC5447885 DOI: 10.1093/jxb/erx077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Meiosis is essential for eukaryotic sexual reproduction and plant fertility. In comparison with over 80 meiotic genes identified in Arabidopsis, there are only ~30 meiotic genes characterized in rice (Oryza sativa L.). Many genes involved in the regulation of meiotic progression remain to be determined. In this study, we identified a sterile rice mutant and cloned a new meiotic gene, OsBVF1 (Bivalent Formation 1) by map-based cloning. Molecular genetics and cytological approaches were carried out to address the function of OsBVF1 in meiosis. Phylogenetic analyses were used to study the evolution of OsBVF1 and its homologs in plant species. Here we showed that the bvf1 male meiocytes were defective in formation of meiotic double strand break, thereby resulting in a failure of bivalent formation in diakinesis and unequal chromosome segregation in anaphase I. The causal gene, OsBVF1, encodes a unique OmpH/coiled-coil motif-containing protein and its homologs are highly conserved in the plant kingdom and seem to be a single-copy gene in the majority of plant species. Our study demonstrates that OsBVF1 is a novel plant-conserved factor involved in meiotic recombination in rice, providing a new insight into understanding of meiotic progression regulation.
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Affiliation(s)
- Lian Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 510642 Guangzhou, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, 510642 Guangzhou, China
- College of Life Sciences, South China Agricultural University, 510642 Guangzhou, China
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Jingluan Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 510642 Guangzhou, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, 510642 Guangzhou, China
- College of Life Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Yuanling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 510642 Guangzhou, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, 510642 Guangzhou, China
- College of Life Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 510642 Guangzhou, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, 510642 Guangzhou, China
- College of Life Sciences, South China Agricultural University, 510642 Guangzhou, China
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Biscotti MA, Canapa A, Forkoni M, Gerdol M, Pallavicini A, Schartl M, Barucca M. The small non-coding RNA processing machinery of two living fossil species, lungfish and coelacanth, gives new insights into the evolution of the Argonaute protein family. Genome Biol Evol 2017; 9:438-453. [PMID: 28206606 PMCID: PMC5381642 DOI: 10.1093/gbe/evx017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 12/21/2016] [Accepted: 02/04/2017] [Indexed: 12/20/2022] Open
Affiliation(s)
- Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona (Italy)
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona (Italy)
| | - Mariko Forkoni
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona (Italy)
| | - Marco Gerdol
- Dipartimento di Scienze della Vita, Università di Trieste (Italy)
| | | | - Manifred Schartl
- Physiological Chemistry, Biocenter, University of Wuerzburg and Comprehensive Cancer Center Mainfranken, University Clinic Wuerzburg, Wuerzburg, Germany; and Texas Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, USA
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona (Italy)
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126
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Wang G, Köhler C. Epigenetic processes in flowering plant reproduction. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:797-807. [PMID: 28062591 DOI: 10.1093/jxb/erw486] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Seeds provide up to 70% of the energy intake of the human population, emphasizing the relevance of understanding the genetic and epigenetic mechanisms controlling seed formation. In flowering plants, seeds are the product of a double fertilization event, leading to the formation of the embryo and the endosperm surrounded by maternal tissues. Analogous to mammals, plants undergo extensive epigenetic reprogramming during both gamete formation and early seed development, a process that is supposed to be required to enforce silencing of transposable elements and thus to maintain genome stability. Global changes of DNA methylation, histone modifications, and small RNAs are closely associated with epigenome programming during plant reproduction. Here, we review current knowledge on chromatin changes occurring during sporogenesis and gametogenesis, as well as early seed development in major flowering plant models.
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Affiliation(s)
- Guifeng Wang
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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127
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Yan W, Chen Z, Lu J, Xu C, Xie G, Li Y, Deng XW, He H, Tang X. Simultaneous Identification of Multiple Causal Mutations in Rice. FRONTIERS IN PLANT SCIENCE 2017; 7:2055. [PMID: 28144247 PMCID: PMC5239786 DOI: 10.3389/fpls.2016.02055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 12/23/2016] [Indexed: 05/26/2023]
Abstract
Next-generation sequencing technologies (NGST) are being used to discover causal mutations in ethyl methanesulfonate (EMS)-mutagenized plant populations. However, the published protocols often deliver too many candidate sites and sometimes fail to find the mutant gene of interest. Accurate identification of the causal mutation from massive background polymorphisms and sequencing deficiencies remains challenging. Here we describe a NGST-based method, named SIMM, that can simultaneously identify the causal mutations in multiple independent mutants. Multiple rice mutants derived from the same parental line were back-crossed, and for each mutant, the derived F2 individuals of the recessive mutant phenotype were pooled and sequenced. The resulting sequences were aligned to the Nipponbare reference genome, and single nucleotide polymorphisms (SNPs) were subsequently compared among the mutants. Allele index (AI) and Euclidean distance (ED) were incorporated into the analysis to reduce noises caused by background polymorphisms and re-sequencing errors. Corrections of sequence bias against GC- and AT-rich sequences in the candidate region were conducted when necessary. Using this method, we successfully identified seven new mutant alleles from Huanghuazhan (HHZ), an elite indica rice cultivar in China. All mutant alleles were validated by phenotype association assay. A pipeline based on Perl scripts for SIMM is publicly available at https://sourceforge.net/projects/simm/.
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Affiliation(s)
- Wei Yan
- College of Life Sciences, Capital Normal UniversityBeijing, China
| | - Zhufeng Chen
- Shenzhen Institute of Molecular Crop DesignShenzhen, China
| | - Jiawei Lu
- Shenzhen Institute of Molecular Crop DesignShenzhen, China
| | - Chunjue Xu
- Shenzhen Institute of Molecular Crop DesignShenzhen, China
| | - Gang Xie
- Shenzhen Institute of Molecular Crop DesignShenzhen, China
| | - Yiqi Li
- Shenzhen Institute of Molecular Crop DesignShenzhen, China
| | - Xing Wang Deng
- Shenzhen Institute of Molecular Crop DesignShenzhen, China
- College of Life Sciences, Peking UniversityBeijing, China
| | - Hang He
- College of Life Sciences, Peking UniversityBeijing, China
| | - Xiaoyan Tang
- Shenzhen Institute of Molecular Crop DesignShenzhen, China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal UniversityGuangzhou, China
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128
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Komiya R. Biogenesis of diverse plant phasiRNAs involves an miRNA-trigger and Dicer-processing. JOURNAL OF PLANT RESEARCH 2017; 130:17-23. [PMID: 27900550 PMCID: PMC5219027 DOI: 10.1007/s10265-016-0878-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/08/2016] [Indexed: 05/18/2023]
Abstract
It has been almost 30 years since RNA interference (RNAi) was shown to silence genes via double-stranded RNAs (dsRNAs) in Caenorhabditis elegans (Fire et al. 1998). 20-30-nucleotide (nt) small non-coding RNAs are a key element of the RNAi machinery. Recently, phased small interfering RNAs (phasiRNAs), small RNAs that are generated from a long RNA precursor at intervals of 21 to 26-nt, have been identified in plants and animals. In Drosophila, phasiRNAs are generated by the endonuclease, Zucchini (Zuc), in germlines. These phasiRNAs, known as one of PIWI-interacting RNAs (piRNAs), mainly repress transposable elements. Similarly, reproduction-specific phasiRNAs have been identified in the family Poaceae, although DICER LIKE (DCL) protein-dependent phasiRNA biogenesis in rice is distinct from piRNA biogenesis in animals. In plants, phasiRNA biogenesis is initiated when 22-nt microRNAs (miRNAs) cleave single-stranded target RNAs. Subsequently, RNA-dependent RNA polymerase (RDR) forms dsRNAs from the cleaved RNAs, and dsRNAs are further processed by DCLs into 21 to 24-nt phasiRNAs. Finally, the phasiRNAs are loaded to ARGONAUTE (AGO) proteins to induce RNA-silencing. There are diverse types of phasiRNA precursors and the miRNAs that trigger the biogenesis. Their expression patterns also differ among plant species, suggesting that species-specific combinations of these triggers dictate the spatio-temporal pattern of phasiRNA biogenesis during development, or in response to environmental stimuli.
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Affiliation(s)
- Reina Komiya
- Science and Technology Group, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Kunigami-gun, Okinawa, 904-0495, Japan.
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129
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PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice. Proc Natl Acad Sci U S A 2016; 113:15144-15149. [PMID: 27965387 DOI: 10.1073/pnas.1619159114] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Phased small-interfering RNAs (phasiRNAs) are a special class of small RNAs, which are generated in 21- or 24-nt intervals from transcripts of precursor RNAs. Although phasiRNAs have been found in a range of organisms, their biological functions in plants have yet to be uncovered. Here we show that phasiRNAs generated by the photopheriod-sensetive genic male sterility 1 (Pms1) locus were associated with photoperiod-sensitive male sterility (PSMS) in rice, a germplasm that started the two-line hybrid rice breeding. The Pms1 locus encodes a long-noncoding RNA PMS1T that was preferentially expressed in young panicles. PMS1T was targeted by miR2118 to produce 21-nt phasiRNAs that preferentially accumulated in the PSMS line under long-day conditions. A single nucleotide polymorphism in PMS1T nearby the miR2118 recognition site was critical for fertility change, likely leading to differential accumulation of the phasiRNAs. This result suggested possible roles of phasiRNAs in reproductive development of rice, demonstrating the potential importance of this RNA class as regulators in biological processes.
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130
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Ta KN, Sabot F, Adam H, Vigouroux Y, De Mita S, Ghesquière A, Do NV, Gantet P, Jouannic S. miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species. RICE (NEW YORK, N.Y.) 2016; 9:10. [PMID: 26969003 PMCID: PMC4788661 DOI: 10.1186/s12284-016-0082-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/06/2016] [Indexed: 05/27/2023]
Abstract
BACKGROUND Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice Oryza glaberrima and its wild relative Oryza barthii. RESULTS Our RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to miR2118-triggered phased siRNAs. A detailed expression profiling during the panicle development of O. glaberrima and O. barthii using qRT-PCRs and in situ hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators (miR2118 and MEL1 gene) in O. glaberrima compared to O. barthii. We provide evidence that the 21-nt phasiRNA pathway in rice is associated with male-gametogenesis but is initiated in spikelet meristems. CONCLUSION Differential expression of the miR2118-triggered 21-nt phasiRNA pathway between the two African rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species.
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Affiliation(s)
- K. N. Ta
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
| | - F. Sabot
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - H. Adam
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - Y. Vigouroux
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - S. De Mita
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
- />Present address: INRA, Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, F-54280 Champenoux, France
| | - A. Ghesquière
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - N. V. Do
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
| | - P. Gantet
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
- />Université de Montpellier, UMR DIADE, Place Eugène Bataillon, F-34095 Montpellier, Cedex 5 France
| | - S. Jouannic
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
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131
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Fei Q, Yang L, Liang W, Zhang D, Meyers BC. Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6037-6049. [PMID: 27702997 PMCID: PMC5100018 DOI: 10.1093/jxb/erw361] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Dissection of the genetic pathways and mechanisms by which anther development occurs in grasses is crucial for both a basic understanding of plant development and for examining traits of agronomic importance such as male sterility. In rice, MULTIPLE SPOROCYTES1 (MSP1), a leucine-rich-repeat receptor kinase, plays an important role in anther development by limiting the number of sporocytes. OsTDL1a (a TPD1-like gene in rice) encodes a small protein that acts as a cofactor of MSP1 in the same regulatory pathway. In this study, we analyzed small RNA and mRNA changes in different stages of spikelets from wild-type rice, and from msp1 and ostdl1a mutants. Analysis of the small RNA data identified miRNAs demonstrating differential abundances. miR2275 was depleted in the two rice mutants; this miRNA is specifically enriched in anthers and functions to trigger the production of 24-nt phased secondary siRNAs (phasiRNAs) from PHAS loci. We observed that the 24-nt phasiRNAs as well as their precursor PHAS mRNAs were also depleted in the two mutants. An analysis of co-expression identified three Argonaute-encoding genes (OsAGO1d, OsAGO2b, and OsAGO18) that accumulate transcripts coordinately with phasiRNAs, suggesting a functional relationship. By mRNA in situ analysis, we demonstrated a strong correlation between the spatiotemporal pattern of these OsAGO transcripts and phasiRNA accumulations.
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Affiliation(s)
- Qili Fei
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Li Yang
- State Key Laboratory of Hybrid Rice, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wanqi Liang
- State Key Laboratory of Hybrid Rice, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dabing Zhang
- State Key Laboratory of Hybrid Rice, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture, Food and Wine, University of Adelaide, South Australia 5064, Australia
| | - Blake C Meyers
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
- University of Missouri - Columbia, Division of Plant Sciences, 52 Agriculture Lab, Columbia, MO 65211, USA
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132
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Yang L, Wu Y, Yu M, Mao B, Zhao B, Wang J. Genome-wide transcriptome analysis of female-sterile rice ovule shed light on its abortive mechanism. PLANTA 2016; 244:1011-1028. [PMID: 27357232 DOI: 10.1007/s00425-016-2563-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/23/2016] [Indexed: 05/03/2023]
Abstract
The comprehensive transcriptome analysis of rice female-sterile line and wild-type line ovule provides an important clue for exploring the regulatory network of the formation of rice fertile female gametophyte. Ovules are the female reproductive tissues of rice (Oryza sativa L.) and play a major role in sexual reproduction. To investigate the potential mechanism of rice female gametophyte fertility, we used RNA sequencing, combined with genetic subtraction, to compare the transcriptome of the ovules of a high-frequency female-sterile line (fsv1) and a rice wild-type line (Gui 99) during ovule development. Ovules were harvested at three developmental stages: ovule containing megaspore mother cell in meiosis process (stage 1), ovule containing functional megaspore in mitosis process (stage 2), and ovule containing mature female gametophyte (stage 3). Six cDNA libraries generated a total of 42.2 million high-quality clean reads that aligned with 30,204 genes. The comparison between the fsv1 and Gui 99 ovules identified a large number of differentially expressed genes (DEGs), i.e., 45, 495, and 932 DEGs at the three ovule developmental stages, respectively. From the comparison of the two rice lines, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and MapMan analyses indicated that a large number of DEGs associated with starch and sucrose metabolism, plant hormone signal transduction, protein modification and degradation, oxidative phosphorylation, and receptor kinase. These DEGs might play roles in ovule development and fertile female gametophyte formation. Many transcription factor genes and epigenetic-related genes also exhibit different expression patterns and significantly different expression levels in two rice lines during ovule development, which might provide important information regarding the abortive mechanism of the female gametophyte in rice.
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Affiliation(s)
- Liyu Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ya Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Meiling Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Bigang Mao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Bingran Zhao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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133
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Rabiger DS, Taylor JM, Spriggs A, Hand ML, Henderson ST, Johnson SD, Oelkers K, Hrmova M, Saito K, Suzuki G, Mukai Y, Carroll BJ, Koltunow AMG. Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation. BMC Biol 2016; 14:86. [PMID: 27716180 PMCID: PMC5054587 DOI: 10.1186/s12915-016-0311-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/21/2016] [Indexed: 11/23/2022] Open
Abstract
Background Application of apomixis, or asexual seed formation, in crop breeding would allow rapid fixation of complex traits, economizing improved crop delivery. Identification of apomixis genes is confounded by the polyploid nature, high genome complexity and lack of genomic sequence integration with reproductive tissue transcriptomes in most apomicts. Results A genomic and transcriptomic resource was developed for Hieracium subgenus Pilosella (Asteraceae) which incorporates characterized sexual, apomictic and mutant apomict plants exhibiting reversion to sexual reproduction. Apomicts develop additional female gametogenic cells that suppress the sexual pathway in ovules. Disrupting small RNA pathways in sexual Arabidopsis also induces extra female gametogenic cells; therefore, the resource was used to examine if changes in small RNA pathways correlate with apomixis initiation. An initial characterization of small RNA pathway genes within Hieracium was undertaken, and ovary-expressed ARGONAUTE genes were identified and cloned. Comparisons of whole ovary transcriptomes from mutant apomicts, relative to the parental apomict, revealed that differentially expressed genes were enriched for processes involved in small RNA biogenesis and chromatin silencing. Small RNA profiles within mutant ovaries did not reveal large-scale alterations in composition or length distributions; however, a small number of differentially expressed, putative small RNA targets were identified. Conclusions The established Hieracium resource represents a substantial contribution towards the investigation of early sexual and apomictic female gamete development, and the generation of new candidate genes and markers. Observed changes in small RNA targets and biogenesis pathways within sexual and apomictic ovaries will underlie future functional research into apomixis initiation in Hieracium. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0311-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David S Rabiger
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Jennifer M Taylor
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Bellenden Street, Crace, Australian Capital Territory, 2911, Australia
| | - Andrew Spriggs
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Bellenden Street, Crace, Australian Capital Territory, 2911, Australia
| | - Melanie L Hand
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Steven T Henderson
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Susan D Johnson
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Karsten Oelkers
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Maria Hrmova
- Australian Centre for Plant Functional Genomics, University of Adelaide PMB 1, Glen Osmond, South Australia, 5064, Australia
| | - Keisuke Saito
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Yasuhiko Mukai
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Anna M G Koltunow
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia.
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134
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A Multigenic Network of ARGONAUTE4 Clade Members Controls Early Megaspore Formation in Arabidopsis. Genetics 2016; 204:1045-1056. [PMID: 27591749 PMCID: PMC5105840 DOI: 10.1534/genetics.116.188151] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/17/2016] [Indexed: 01/01/2023] Open
Abstract
The development of gametophytes relies on the establishment of a haploid gametophytic generation that initiates with the specification of gametophytic precursors. The majority of flowering plants differentiate a single gametophytic precursor in the ovule: the megaspore mother cell. Here we show that, in addition to argonaute9 (ago9), mutations in other ARGONAUTE (AGO) genes such as ago4, ago6, and ago8, also show abnormal configurations containing supernumerary gametophytic precursors in Arabidopsis thaliana. Double homozygous ago4 ago9 individuals showed a suppressive effect on the frequency of ovules with multiple gametophytic precursors across three consecutive generations, indicating that genetic interactions result in compensatory mechanisms. Whereas overexpression of AGO6 in ago9 and ago4 ago9 confirms strong regulatory interactions among genes involved in RNA-directed DNA methylation, AGO8 is overexpressed in premeiotic ovules of ago4 ago9 individuals, suggesting that the regulation of this previously presumed pseudogene responds to the compensatory mechanism. The frequency of abnormal meiotic configurations found in ago4 ago9 individuals is dependent on their parental genotype, revealing a transgenerational effect. Our results indicate that members of the AGO4 clade cooperatively participate in preventing the abnormal specification of multiple premeiotic gametophytic precursors during early ovule development in A. thaliana.
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135
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Liu H, Nonomura KI. A wide reprogramming of histone H3 modifications during male meiosis I in rice is dependent on the Argonaute protein MEL1. J Cell Sci 2016; 129:3553-3561. [PMID: 27521428 DOI: 10.1242/jcs.184937] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 08/05/2016] [Indexed: 12/11/2022] Open
Abstract
The roles of epigenetic mechanisms, including small-RNA-mediated silencing, in plant meiosis largely remain unclear, despite their importance in plant reproduction. This study unveiled that rice chromosomes are reprogrammed during the premeiosis-to-meiosis transition in pollen mother cells (PMCs). This large-scale meiotic chromosome reprogramming (LMR) continued throughout meiosis I, during which time H3K9 dimethylation (H3K9me2) was increased, and H3K9 acetylation and H3S10 phosphorylation were broadly decreased, with an accompanying immunostaining pattern shift of RNA polymerase II. LMR was dependent on the rice Argonaute protein, MEIOSIS ARRESTED AT LEPTOTENE1 (MEL1), which is specifically expressed in germ cells prior to meiosis, because LMR was severely diminished in mel1 mutant anthers. Pivotal meiotic events, such as pre-synaptic centromere association, DNA double-strand break initiation and synapsis of homologous chromosomes, were also disrupted in this mutant. Interestingly, and as opposed to the LMR loss in most chromosomal regions, aberrant meiotic protein loading and hypermethylation of H3K9 emerged on the nucleolar organizing region in the mel1 PMCs. These results suggest that MEL1 plays important roles in epigenetic LMR to promote faithful homologous recombination and synapsis during rice meiosis.
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Affiliation(s)
- Hua Liu
- Experimental Farm, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Ken-Ichi Nonomura
- Experimental Farm, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan Department of Life Science, Graduate University for Advanced Studies/SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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136
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Huang J, Li Z, Zhao D. Deregulation of the OsmiR160 Target Gene OsARF18 Causes Growth and Developmental Defects with an Alteration of Auxin Signaling in Rice. Sci Rep 2016; 6:29938. [PMID: 27444058 PMCID: PMC4956771 DOI: 10.1038/srep29938] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/27/2016] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) control gene expression as key negative regulators at the post-transcriptional level. MiR160 plays a pivotal role in Arabidopsis growth and development through repressing expression of its target AUXIN RESPONSE FACTOR (ARF) genes; however, the function of miR160 in monocots remains elusive. In this study, we found that the mature rice miR160 (OsmiR160) was mainly derived from OsMIR160a and OsMIR160b genes. Among four potential OsmiR160 target OsARF genes, the OsARF18 transcript was cleaved at the OsmiR160 target site. Rice transgenic plants (named mOsARF18) expressing an OsmiR160-resistant version of OsARF18 exhibited pleiotropic defects in growth and development, including dwarf stature, rolled leaves, and small seeds. mOsARF18 leaves were abnormal in bulliform cell differentiation and epidermal cell division. Starch accumulation in mOsARF18 seeds was also reduced. Moreover, auxin induced expression of OsMIR160a, OsMIR160b, and OsARF18, whereas expression of OsMIR160a and OsMIR160b as well as genes involved in auxin signaling was altered in mOsARF18 plants. Our results show that negative regulation of OsARF18 expression by OsmiR160 is critical for rice growth and development via affecting auxin signaling, which will advance future studies on the molecular mechanism by which miR160 fine-tunes auxin signaling in plants.
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Affiliation(s)
- Jian Huang
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Zhiyong Li
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Dazhong Zhao
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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137
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Azlan A, Dzaki N, Azzam G. Argonaute: The executor of small RNA function. J Genet Genomics 2016; 43:481-94. [PMID: 27569398 DOI: 10.1016/j.jgg.2016.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/08/2016] [Accepted: 06/17/2016] [Indexed: 01/06/2023]
Abstract
The discovery of small non-coding RNAs - microRNA (miRNA), short interfering RNA (siRNA) and PIWI-interacting RNA (piRNA) - represents one of the most exciting frontiers in biology specifically on the mechanism of gene regulation. In order to execute their functions, these small RNAs require physical interactions with their protein partners, the Argonaute (AGO) family proteins. Over the years, numerous studies have made tremendous progress on understanding the roles of AGO in gene silencing in various organisms. In this review, we summarize recent progress of AGO-mediated gene silencing and other cellular processes in which AGO proteins have been implicated with a particular focus on progress made in flies, humans and other model organisms as compliment.
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Affiliation(s)
- Azali Azlan
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Najat Dzaki
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Ghows Azzam
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia; Advance Medical and Dental Institute, Universiti Sains Malaysia, Penang 11800, Malaysia.
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138
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Xin Q, Shen Y, Li X, Lu W, Wang X, Han X, Dong F, Wan L, Yang G, Hong D, Cheng Z. MS5 Mediates Early Meiotic Progression and Its Natural Variants May Have Applications for Hybrid Production in Brassica napus. THE PLANT CELL 2016; 28:1263-78. [PMID: 27194707 PMCID: PMC4944402 DOI: 10.1105/tpc.15.01018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/16/2016] [Indexed: 05/02/2023]
Abstract
During meiotic prophase I, chromatin undergoes dynamic changes to establish a structural basis for essential meiotic events. However, the mechanism that coordinates chromosome structure and meiotic progression remains poorly understood in plants. Here, we characterized a spontaneous sterile mutant MS5(b)MS5(b) in oilseed rape (Brassica napus) and found its meiotic chromosomes were arrested at leptotene. MS5 is preferentially expressed in reproductive organs and encodes a Brassica-specific protein carrying conserved coiled-coil and DUF626 domains with unknown function. MS5 is essential for pairing of homologs in meiosis, but not necessary for the initiation of DNA double-strand breaks. The distribution of the axis element-associated protein ASY1 occurs independently of MS5, but localization of the meiotic cohesion subunit SYN1 requires functional MS5. Furthermore, both the central element of the synaptonemal complex and the recombination element do not properly form in MS5(b)MS5(b) mutants. Our results demonstrate that MS5 participates in progression of meiosis during early prophase I and its allelic variants lead to differences in fertility, which may provide a promising strategy for pollination control for heterosis breeding.
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Affiliation(s)
- Qiang Xin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Shen
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xi Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Lu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China College of Life Science, South-central University for Nationalities, Wuhan 430074, China
| | - Xiang Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xue Han
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Faming Dong
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lili Wan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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139
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Liu X, Tang S, Jia G, Schnable JC, Su H, Tang C, Zhi H, Diao X. The C-terminal motif of SiAGO1b is required for the regulation of growth, development and stress responses in foxtail millet (Setaria italica (L.) P. Beauv). JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3237-49. [PMID: 27045099 PMCID: PMC4892719 DOI: 10.1093/jxb/erw135] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Foxtail millet (Setaria italica (L.) P. Beauv), which belongs to the Panicoideae tribe of the Poaceae, is an important grain crop widely grown in Northern China and India. It is currently developing into a novel model species for functional genomics of the Panicoideae as a result of its fully available reference genome sequence, small diploid genome (2n=18, ~510Mb), short life cycle, small stature and prolific seed production. Argonaute 1 (AGO1), belonging to the argonaute (AGO) protein family, recruits small RNAs and regulates plant growth and development. Here, we characterized an AGO1 mutant (siago1b) in foxtail millet, which was induced by ethyl methanesulfonate treatment. The mutant exhibited pleiotropic developmental defects, including dwarfing stem, narrow and rolled leaves, smaller panicles and lower rates of seed setting. Map-based cloning analysis demonstrated that these phenotypic variations were attributed to a C-A transversion, and a 7-bp deletion in the C-terminus of the SiAGO1b gene in siago1b Yeast two-hybrid assays and BiFC experiments revealed that the mutated region was an essential functional motif for the interaction between SiAGO1b and SiHYL1. Furthermore, 1598 differentially expressed genes were detected via RNA-seq-based comparison of SiAGO1b and wild-type plants, which revealed that SiAGO1b mutation influenced multiple biological processes, including energy metabolism, cell growth, programmed death and abiotic stress responses in foxtail millet. This study may provide a better understanding of the mechanisms by which SiAGO1b regulates the growth and development of crops.
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Affiliation(s)
- Xiaotong Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - James C Schnable
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China. Agronomy & Horticulture, University of Nebraska-Lincoln, Beadle Center E207, Lincoln, NE 68583-0660, USA
| | - Haixia Su
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chanjuan Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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140
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Walbot V, Egger RL. Pre-Meiotic Anther Development: Cell Fate Specification and Differentiation. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:365-95. [PMID: 26735065 DOI: 10.1146/annurev-arplant-043015-111804] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Research into anther ontogeny has been an active and developing field, transitioning from a strictly lineage-based view of cellular differentiation events to a more complex understanding of cell fate specification. Here we describe the modern interpretation of pre-meiotic anther development, from the earliest cell specifications within the anther lobes through SPL/NZZ-, MSP1-, and MEL1-dependent pathways as well as the initial setup of the abaxial and adaxial axes and outgrowth of the anther lobes. We then continue with a look at the known information regarding further differentiation of the somatic layers of the anther (the epidermis, endothecium, middle layer, and tapetum), with an emphasis on male-sterile mutants identified as defective in somatic cell specification. We also describe the differences in developmental stages among species and use this information to discuss molecular studies that have analyzed transcriptome, proteome, and small-RNA information in the anther.
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Affiliation(s)
- Virginia Walbot
- Department of Biology, Stanford University, Stanford, California 94305-5020; ,
| | - Rachel L Egger
- Department of Biology, Stanford University, Stanford, California 94305-5020; ,
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141
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Li X, Shahid MQ, Wu J, Wang L, Liu X, Lu Y. Comparative Small RNA Analysis of Pollen Development in Autotetraploid and Diploid Rice. Int J Mol Sci 2016; 17:499. [PMID: 27077850 PMCID: PMC4848955 DOI: 10.3390/ijms17040499] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/24/2016] [Accepted: 03/28/2016] [Indexed: 11/21/2022] Open
Abstract
MicroRNAs (miRNAs) play key roles in plant reproduction. However, knowledge on microRNAome analysis in autotetraploid rice is rather limited. Here, high-throughput sequencing technology was employed to analyze miRNAomes during pollen development in diploid and polyploid rice. A total of 172 differentially expressed miRNAs (DEM) were detected in autotetraploid rice compared to its diploid counterpart, and 57 miRNAs were specifically expressed in autotetraploid rice. Of the 172 DEM, 115 and 61 miRNAs exhibited up- and down-regulation, respectively. Gene Ontology analysis on the targets of up-regulated DEM showed that they were enriched in transport and membrane in pre-meiotic interphase, reproduction in meiosis, and nucleotide binding in single microspore stage. osa-miR5788 and osa-miR1432-5p_R+1 were up-regulated in meiosis and their targets revealed interaction with the meiosis-related genes, suggesting that they may involve in the genes regulation associated with the chromosome behavior. Abundant 24 nt siRNAs associated with transposable elements were found in autotetraploid rice during pollen development; however, they significantly declined in diploid rice, suggesting that 24 nt siRNAs may play a role in pollen development. These findings provide a foundation for understanding the effect of polyploidy on small RNA expression patterns during pollen development that cause pollen sterility in autotetraploid rice.
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Affiliation(s)
- Xiang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Lan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Yonggen Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
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142
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Gerson-Gurwitz A, Wang S, Sathe S, Green R, Yeo GW, Oegema K, Desai A. A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions. Cell 2016; 165:396-409. [PMID: 27020753 DOI: 10.1016/j.cell.2016.02.040] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/20/2016] [Accepted: 02/18/2016] [Indexed: 12/11/2022]
Abstract
Multiple division cycles without growth are a characteristic feature of early embryogenesis. The female germline loads proteins and RNAs into oocytes to support these divisions, which lack many quality control mechanisms operating in somatic cells undergoing growth. Here, we describe a small RNA-Argonaute pathway that ensures early embryonic divisions in C. elegans by employing catalytic slicing activity to broadly tune, instead of silence, germline gene expression. Misregulation of one target, a kinesin-13 microtubule depolymerase, underlies a major phenotype associated with pathway loss. Tuning of target transcript levels is guided by the density of homologous small RNAs, whose generation must ultimately be related to target sequence. Thus, the tuning action of a small RNA-catalytic Argonaute pathway generates oocytes capable of supporting embryogenesis. We speculate that the specialized nature of germline chromatin led to the emergence of small RNA-catalytic Argonaute pathways in the female germline as a post-transcriptional control layer to optimize oocyte composition.
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Affiliation(s)
- Adina Gerson-Gurwitz
- Ludwig Institute for Cancer Research, San Diego, CA 92093, USA; Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Shaohe Wang
- Ludwig Institute for Cancer Research, San Diego, CA 92093, USA; Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Shashank Sathe
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; UCSD Stem Cell Program & Sanford Consortium for Regenerative Medicine, Institute for Genomic Medicine, La Jolla, CA 92093, USA
| | - Rebecca Green
- Ludwig Institute for Cancer Research, San Diego, CA 92093, USA; Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA; UCSD Stem Cell Program & Sanford Consortium for Regenerative Medicine, Institute for Genomic Medicine, La Jolla, CA 92093, USA
| | - Karen Oegema
- Ludwig Institute for Cancer Research, San Diego, CA 92093, USA; Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Arshad Desai
- Ludwig Institute for Cancer Research, San Diego, CA 92093, USA; Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA.
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143
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Ma X, Tang Z, Qin J, Meng Y. The use of high-throughput sequencing methods for plant microRNA research. RNA Biol 2016; 12:709-19. [PMID: 26016494 DOI: 10.1080/15476286.2015.1053686] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
MicroRNA (miRNA) acts as a critical regulator of gene expression at post-transcriptional and occasionally transcriptional levels in plants. Identification of reliable miRNA genes, monitoring the procedures of transcription, processing and maturation of the miRNAs, quantification of the accumulation levels of the miRNAs in specific biological samples, and validation of miRNA-target interactions become the basis for thoroughly understanding of the miRNA-mediated regulatory networks and the underlying mechanisms. Great progresses have been achieved for sequencing technology. Based on the high degree of sequencing depth and coverage, the high-throughput sequencing (HTS, also called next-generation sequencing) technology provides unprecedentedly efficient way for genome-wide or transcriptome-wide studies. In this review, we will introduce several HTS platform-based methods useful for plant miRNA research, including RNA-seq (RNA sequencing), RNA-PET-seq (paired end tag sequencing of RNAs), sRNA-seq (small RNA sequencing), dsRNA-seq (double-stranded RNA sequencing), ssRNA-seq (single-stranded RNA sequencing) and degradome-seq (degradome sequencing). In particular, we will provide some special cases to illustrate the novel use of HTS methods for investigation of the processing modes of the miRNA precursors, identification of the RNA editing sites on miRNA precursors, mature miRNAs and target transcripts, re-examination of the current miRNA registries, and discovery of novel miRNA species and novel miRNA-target interactions. Summarily, we opinioned that integrative use of the above mentioned HTS methods could make the studies on miRNAs more efficient.
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Affiliation(s)
- Xiaoxia Ma
- a College of Life and Environmental Sciences; Hangzhou Normal University ; Hangzhou , PR China
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144
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Zhai L, Wang L, Teng F, Zhou L, Zhang W, Xiao J, Liu Y, Deng W. Argonaute and Argonaute-Bound Small RNAs in Stem Cells. Int J Mol Sci 2016; 17:208. [PMID: 26861290 PMCID: PMC4783940 DOI: 10.3390/ijms17020208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 01/28/2016] [Accepted: 02/01/2016] [Indexed: 12/15/2022] Open
Abstract
Small RNAs are essential for a variety of cellular functions. Argonaute (AGO) proteins are associated with all of the different classes of small RNAs, and are indispensable in small RNA-mediated regulatory pathways. AGO proteins have been identified in various types of stem cells in diverse species from plants and animals. This review article highlights recent progress on how AGO proteins and AGO-bound small RNAs regulate the self-renewal and differentiation of distinct stem cell types, including pluripotent, germline, somatic, and cancer stem cells.
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Affiliation(s)
- Lihong Zhai
- Medical College, Hubei University of Arts and Science, Xiangyang 441053, Hubei, China.
| | - Lin Wang
- Xiangyang Oral Hospital, Xiangyang 441003, Hubei, China.
| | - Feng Teng
- Medical College, Hubei University of Arts and Science, Xiangyang 441053, Hubei, China.
| | - Lanting Zhou
- Medical College, Hubei University of Arts and Science, Xiangyang 441053, Hubei, China.
| | - Wenjing Zhang
- Medical College, Hubei University of Arts and Science, Xiangyang 441053, Hubei, China.
| | - Juan Xiao
- Medical College, Hubei University of Arts and Science, Xiangyang 441053, Hubei, China.
| | - Ying Liu
- Department of Neurosurgery, Medical School, the Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
- Center for Stem Cell and Regenerative Medicine, the Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Wenbin Deng
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA 95817, USA.
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Sacramento, CA 95817, USA.
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145
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Fang X, Qi Y. RNAi in Plants: An Argonaute-Centered View. THE PLANT CELL 2016; 28:272-85. [PMID: 26869699 PMCID: PMC4790879 DOI: 10.1105/tpc.15.00920] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/29/2015] [Accepted: 02/10/2016] [Indexed: 05/18/2023]
Abstract
Argonaute (AGO) family proteins are effectors of RNAi in eukaryotes. AGOs bind small RNAs and use them as guides to silence target genes or transposable elements at the transcriptional or posttranscriptional level. Eukaryotic AGO proteins share common structural and biochemical properties and function through conserved core mechanisms in RNAi pathways, yet plant AGOs have evolved specialized and diversified functions. This Review covers the general features of AGO proteins and highlights recent progress toward our understanding of the mechanisms and functions of plant AGOs.
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Affiliation(s)
- Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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146
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Rodríguez-Leal D, Castillo-Cobián A, Rodríguez-Arévalo I, Vielle-Calzada JP. A Primary Sequence Analysis of the ARGONAUTE Protein Family in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1347. [PMID: 27635128 PMCID: PMC5007885 DOI: 10.3389/fpls.2016.01347] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 08/22/2016] [Indexed: 05/08/2023]
Abstract
Small RNA (sRNA)-mediated gene silencing represents a conserved regulatory mechanism controlling a wide diversity of developmental processes through interactions of sRNAs with proteins of the ARGONAUTE (AGO) family. On the basis of a large phylogenetic analysis that includes 206 AGO genes belonging to 23 plant species, AGO genes group into four clades corresponding to the phylogenetic distribution proposed for the ten family members of Arabidopsis thaliana. A primary analysis of the corresponding protein sequences resulted in 50 sequences of amino acids (blocks) conserved across their linear length. Protein members of the AGO4/6/8/9 and AGO1/10 clades are more conserved than members of the AGO5 and AGO2/3/7 clades. In addition to blocks containing components of the PIWI, PAZ, and DUF1785 domains, members of the AGO2/3/7 and AGO4/6/8/9 clades possess other consensus block sequences that are exclusive of members within these clades, suggesting unforeseen functional specialization revealed by their primary sequence. We also show that AGO proteins of animal and plant kingdoms share linear sequences of blocks that include motifs involved in posttranslational modifications such as those regulating AGO2 in humans and the PIWI protein AUBERGINE in Drosophila. Our results open possibilities for exploring new structural and functional aspects related to the evolution of AGO proteins within the plant kingdom, and their convergence with analogous proteins in mammals and invertebrates.
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Affiliation(s)
- Daniel Rodríguez-Leal
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV IrapuatoIrapuato, Mexico
- Departamento de Ingeniería Genética de Plantas, CINVESTAV IrapuatoIrapuato, Mexico
| | | | - Isaac Rodríguez-Arévalo
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV IrapuatoIrapuato, Mexico
| | - Jean-Philippe Vielle-Calzada
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV IrapuatoIrapuato, Mexico
- *Correspondence: Jean-Philippe Vielle-Calzada
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147
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Dukowic-Schulze S, Sundararajan A, Ramaraj T, Kianian S, Pawlowski WP, Mudge J, Chen C. Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis. FRONTIERS IN PLANT SCIENCE 2016; 7:762. [PMID: 27313591 PMCID: PMC4889585 DOI: 10.3389/fpls.2016.00762] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/17/2016] [Indexed: 05/03/2023]
Abstract
Small RNAs (sRNA) add additional layers to the regulation of gene expression, with siRNAs directing gene silencing at the DNA level by RdDM (RNA-directed DNA methylation), and micro RNAs (miRNAs) directing post-transcriptional regulation of specific target genes, mostly by mRNA cleavage. We used manually isolated male meiocytes from maize (Zea mays) to investigate sRNA and DNA methylation landscapes during zygotene, an early stage of meiosis during which steps of meiotic recombination and synapsis of paired homologous chromosomes take place. We discovered two novel miRNAs from meiocytes, zma-MIR11969 and zma-MIR11970, and identified putative target genes. Furthermore, we detected abundant phasiRNAs of 21 and 24 nt length. PhasiRNAs are phased small RNAs which occur in 21 or 24 nt intervals, at a few hundred loci, specifically in male reproductive tissues in grasses. So far, the function of phasiRNAs remained elusive. Data from isolated meiocytes now revealed elevated DNA methylation at phasiRNA loci, especially in the CHH context, suggesting a role for phasiRNAs in cis DNA methylation. In addition, we consider a role of these phasiRNAs in chromatin remodeling/dynamics during meiosis. However, this is not well supported yet and will need more additional data. Here, we only lay out the idea due to other relevant literature and our additional observation of a peculiar GC content pattern at phasiRNA loci. Chromatin remodeling is also indicated by the discovery that histone genes were enriched for sRNA of 22 nt length. Taken together, we gained clues that lead us to hypothesize sRNA-driven DNA methylation and possibly chromatin remodeling during male meiosis in the monocot maize which is in line with and extends previous knowledge.
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Affiliation(s)
| | | | | | - Shahryar Kianian
- Cereal Disease Laboratory, United States Department of Agriculture – Agricultural Research Service, St. PaulMN, USA
| | - Wojciech P. Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa FeNM, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. PaulMN, USA
- *Correspondence: Changbin Chen,
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148
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Mattiello L, Riaño-Pachón DM, Martins MCM, da Cruz LP, Bassi D, Marchiori PER, Ribeiro RV, Labate MTV, Labate CA, Menossi M. Physiological and transcriptional analyses of developmental stages along sugarcane leaf. BMC PLANT BIOLOGY 2015; 15:300. [PMID: 26714767 PMCID: PMC4696237 DOI: 10.1186/s12870-015-0694-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/17/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sugarcane is one of the major crops worldwide. It is cultivated in over 100 countries on 22 million ha. The complex genetic architecture and the lack of a complete genomic sequence in sugarcane hamper the adoption of molecular approaches to study its physiology and to develop new varieties. Investments on the development of new sugarcane varieties have been made to maximize sucrose yield, a trait dependent on photosynthetic capacity. However, detailed studies on sugarcane leaves are scarce. In this work, we report the first molecular and physiological characterization of events taking place along a leaf developmental gradient in sugarcane. RESULTS Photosynthetic response to CO2 indicated divergence in photosynthetic capacity based on PEPcase activity, corroborated by activity quantification (both in vivo and in vitro) and distinct levels of carbon discrimination on different segments along leaf length. Additionally, leaf segments had contrasting amount of chlorophyll, nitrogen and sugars. RNA-Seq data indicated a plethora of biochemical pathways differentially expressed along the leaf. Some transcription factors families were enriched on each segment and their putative functions corroborate with the distinct developmental stages. Several genes with higher expression in the middle segment, the one with the highest photosynthetic rates, were identified and their role in sugarcane productivity is discussed. Interestingly, sugarcane leaf segments had a different transcriptional behavior compared to previously published data from maize. CONCLUSION This is the first report of leaf developmental analysis in sugarcane. Our data on sugarcane is another source of information for further studies aiming to understand and/or improve C4 photosynthesis. The segments used in this work were distinct in their physiological status allowing deeper molecular analysis. Although limited in some aspects, the comparison to maize indicates that all data acquired on one C4 species cannot always be easily extrapolated to other species. However, our data indicates that some transcriptional factors were segment-specific and the sugarcane leaf undergoes through the process of suberizarion, photosynthesis establishment and senescence.
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Affiliation(s)
- Lucia Mattiello
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
- Laboratório de Genoma Funcional, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Caixa Postal 6109, Campinas, 13083-862, SP, Brazil.
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Marina Camara Mattos Martins
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Larissa Prado da Cruz
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Denis Bassi
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Paulo Eduardo Ribeiro Marchiori
- Laboratório de Fisiologia de Plantas "Coaracy M. Franco", Centro de Pesquisa e Desenvolvimento em Ecofisiologia e Biofísica, Instituto Agronômico, Caixa Postal 28, Campinas, 13020-902, SP, Brazil.
| | - Rafael Vasconcelos Ribeiro
- Departamento de Biologia de Plantas, Universidade Estadual de Campinas, Caixa Postal 6109, Campinas, 13083-970, SP, Brazil.
| | - Mônica T Veneziano Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Universidade de São Paulo, Caixa Postal 83, Piracicaba, 13400-970, SP, Brazil.
| | - Carlos Alberto Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Universidade de São Paulo, Caixa Postal 83, Piracicaba, 13400-970, SP, Brazil.
| | - Marcelo Menossi
- Laboratório de Genoma Funcional, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Caixa Postal 6109, Campinas, 13083-862, SP, Brazil.
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Zhang C, Wu Z, Li Y, Wu J. Biogenesis, Function, and Applications of Virus-Derived Small RNAs in Plants. Front Microbiol 2015; 6:1237. [PMID: 26617580 PMCID: PMC4637412 DOI: 10.3389/fmicb.2015.01237] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
RNA silencing, an evolutionarily conserved and sequence-specific gene-inactivation system, has a pivotal role in antiviral defense in most eukaryotic organisms. In plants, a class of exogenous small RNAs (sRNAs) originating from the infecting virus called virus-derived small interfering RNAs (vsiRNAs) are predominantly responsible for RNA silencing-mediated antiviral immunity. Nowadays, the process of vsiRNA formation and the role of vsiRNAs in plant viral defense have been revealed through deep sequencing of sRNAs and diverse genetic analysis. The biogenesis of vsiRNAs is analogous to that of endogenous sRNAs, which require diverse essential components including dicer-like (DCL), argonaute (AGO), and RNA-dependent RNA polymerase (RDR) proteins. vsiRNAs trigger antiviral defense through post-transcriptional gene silencing (PTGS) or transcriptional gene silencing (TGS) of viral RNA, and they hijack the host RNA silencing system to target complementary host transcripts. Additionally, several applications that take advantage of the current knowledge of vsiRNAs research are being used, such as breeding antiviral plants through genetic engineering technology, reconstructing of viral genomes, and surveying viral ecology and populations. Here, we will provide an overview of vsiRNA pathways, with a primary focus on the advances in vsiRNA biogenesis and function, and discuss their potential applications as well as the future challenges in vsiRNAs research.
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Affiliation(s)
- Chao Zhang
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zujian Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Yi Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, China
| | - Jianguo Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China ; Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, China
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Abstract
Plant genomes encode various small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small-RNA classes varies among plant species, suggesting coevolution between environmental adaptations and gene-silencing mechanisms. Biogenesis of small RNAs in plants is well understood, but we are just beginning to uncover their intricate regulation and activity. Here, we discuss the biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNAs, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation. We also discuss the diversification of small-RNA-directed silencing pathways through the expansion of RNA-dependent RNA polymerases, DICER proteins and ARGONAUTE proteins.
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