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Russell SD, Gou X, Wong CE, Wang X, Yuan T, Wei X, Bhalla PL, Singh MB. Genomic profiling of rice sperm cell transcripts reveals conserved and distinct elements in the flowering plant male germ lineage. THE NEW PHYTOLOGIST 2012; 195:560-573. [PMID: 22716952 DOI: 10.1111/j.1469-8137.2012.04199.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Genomic assay of sperm cell RNA provides insight into functional control, modes of regulation, and contributions of male gametes to double fertilization. Sperm cells of rice (Oryza sativa) were isolated from field-grown, disease-free plants and RNA was processed for use with the full-genome Affymetrix microarray. Comparison with Gene Expression Omnibus (GEO) reference arrays confirmed expressionally distinct gene profiles. A total of 10,732 distinct gene sequences were detected in sperm cells, of which 1668 were not expressed in pollen or seedlings. Pathways enriched in male germ cells included ubiquitin-mediated pathways, pathways involved in chromatin modeling including histones, histone modification and nonhistone epigenetic modification, and pathways related to RNAi and gene silencing. Genome-wide expression patterns in angiosperm sperm cells indicate common and divergent themes in the male germline that appear to be largely self-regulating through highly up-regulated chromatin modification pathways. A core of highly conserved genes appear common to all sperm cells, but evidence is still emerging that another class of genes have diverged in expression between monocots and dicots since their divergence. Sperm cell transcripts present at fusion may be transmitted through plasmogamy during double fertilization to effect immediate post-fertilization expression of early embryo and (or) endosperm development.
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Affiliation(s)
- Scott D Russell
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Xiaoping Gou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Chui E Wong
- Plant Molecular Biology and Biotechnology Laboratory, Australian Research Council Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Xinkun Wang
- Higuchi Biosciences Center, University of Kansas, Lawrence, KS 66047, USA
| | - Tong Yuan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Xiaoping Wei
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Australian Research Council Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Australian Research Council Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, University of Melbourne, Parkville, Victoria 3010, Australia
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202
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Thiebaut F, Grativol C, Carnavale-Bottino M, Rojas CA, Tanurdzic M, Farinelli L, Martienssen RA, Hemerly AS, Ferreira PCG. Computational identification and analysis of novel sugarcane microRNAs. BMC Genomics 2012; 13:290. [PMID: 22747909 PMCID: PMC3464620 DOI: 10.1186/1471-2164-13-290] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 05/02/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNA-regulation of gene expression plays a key role in the development and response to biotic and abiotic stresses. Deep sequencing analyses accelerate the process of small RNA discovery in many plants and expand our understanding of miRNA-regulated processes. We therefore undertook small RNA sequencing of sugarcane miRNAs in order to understand their complexity and to explore their role in sugarcane biology. RESULTS A bioinformatics search was carried out to discover novel miRNAs that can be regulated in sugarcane plants submitted to drought and salt stresses, and under pathogen infection. By means of the presence of miRNA precursors in the related sorghum genome, we identified 623 candidates of new mature miRNAs in sugarcane. Of these, 44 were classified as high confidence miRNAs. The biological function of the new miRNAs candidates was assessed by analyzing their putative targets. The set of bona fide sugarcane miRNA includes those likely targeting serine/threonine kinases, Myb and zinc finger proteins. Additionally, a MADS-box transcription factor and an RPP2B protein, which act in development and disease resistant processes, could be regulated by cleavage (21-nt-species) and DNA methylation (24-nt-species), respectively. CONCLUSIONS A large scale investigation of sRNA in sugarcane using a computational approach has identified a substantial number of new miRNAs and provides detailed genotype-tissue-culture miRNA expression profiles. Comparative analysis between monocots was valuable to clarify aspects about conservation of miRNA and their targets in a plant whose genome has not yet been sequenced. Our findings contribute to knowledge of miRNA roles in regulatory pathways in the complex, polyploidy sugarcane genome.
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Affiliation(s)
- Flávia Thiebaut
- Laboratorio de Biologia Molecular de Plantas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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203
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Chen X. Small RNAs in development - insights from plants. Curr Opin Genet Dev 2012; 22:361-7. [PMID: 22578318 DOI: 10.1016/j.gde.2012.04.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 03/30/2012] [Accepted: 04/11/2012] [Indexed: 10/28/2022]
Abstract
microRNAs (miRNAs) and small interfering RNAs (siRNAs), which constitute two major classes of endogenous small RNAs in plants, impact a multitude of developmental and physiological processes by imparting sequence specificity to gene and genome regulation. Although lacking the third major class of small RNAs found in animals, Piwi-interacting RNAs (piRNAs), plants have expanded their repertoire of endogenous siRNAs, some of which fulfill similar molecular and developmental functions as piRNAs in animals. Research on plant miRNAs and siRNAs has contributed invaluable insights into small RNA biology, thanks to the highly conserved molecular logic behind the biogenesis and actions of small RNAs. Here, I review progress in the plant small RNA field in the past two years, with an emphasis on recent findings related to plant development. I do not recount the numerous developmental processes regulated by small RNAs; instead, I focus on major principles that have been derived from recent studies and draw parallels, when applicable, between plants and animals.
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Affiliation(s)
- Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, United States.
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204
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Gutierrez-Marcos JF, Dickinson HG. Epigenetic reprogramming in plant reproductive lineages. PLANT & CELL PHYSIOLOGY 2012; 53:817-23. [PMID: 22505692 DOI: 10.1093/pcp/pcs052] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Monoecious flowering plants produce both microgametophytes (pollen) and megagametophytes (embryo sacs) containing the male and female gametes, respectively, which participate in double fertilization. Much is known about cellular and developmental processes giving rise to these reproductive structures and the formation of gametes. However, little is known about the role played by changes in the epigenome in dynamically shaping these defining events during plant sexual reproduction. This has in part been hampered by the inaccessibility of these structures-especially the female gametes, which are embedded within the female reproductive tissues of the plant sporophyte. However, with the recent development of new cellular isolation technologies that can be coupled to next-generation sequencing, a new wave of epigenomic studies indicate that an intricate epigenetic regulation takes place during the formation of male and female reproductive lineages. In this mini review, we assess the fast growing body of evidence for the epigenetic regulation of the developmental fate and function of plant gametes. We describe how small interfereing RNAs and DNA methylation machinery play a part in setting up unique epigenetic landscapes in different gametes, which may be responsible for their different fates and functions during fertilization. Collectively these studies will shed light on the dynamic epigenomic landscape of plant gametes or 'epigametes' and help to answer important unresolved questions on the sexual reproduction of flowering plants, especially those underpinning the formation of two products of fertilization, the embryo and the endosperm.
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205
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Yi J, Kim SR, Lee DY, Moon S, Lee YS, Jung KH, Hwang I, An G. The rice gene DEFECTIVE TAPETUM AND MEIOCYTES 1 (DTM1) is required for early tapetum development and meiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:256-70. [PMID: 22111585 DOI: 10.1111/j.1365-313x.2011.04864.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Tapetum development and meiosis play crucial roles in anther development. Here we identified a rice gene, DEFECTIVE TAPETUM AND MEIOCYTES 1 (DTM1), which controls the early stages of that development. This gene encodes for an endoplasmic reticulum (ER) membrane protein that is present only in cereals. Our T-DNA insertion mutations gave rise to abnormal tapetal formation. Cellular organelles, especially the ER, were underdeveloped, which led to hampered differentiation and degeneration of the tapetum. In addition, the development of pollen mother cells was arrested at the early stages of meiotic prophase I. RNA in-situ hybridization analyses showed that DTM1 transcripts were most abundant in tapetal cells at stages 6 and 7, and moderately in the pollen mother cells and meiocytes. Transcripts of UDT1, which functions in tapetum development during early meiosis, were reduced in dtm1 anthers, as were those of PAIR1, which is involved in chromosome pairing and synapsis during meiosis. However, expression of MSP1 and MEL1, which function in anther wall specification and germ cell division, respectively, was not altered in the dtm1 mutant. Moreover, transcripts of DTM1 were reduced in msp1 mutant anthers, but not in udt1 and pair1 mutants. These results, together with their mutant phenotypes, suggest that DTM1 plays important roles in the ER membrane during early tapetum development, functioning after MSP1 and before UDT1, and also in meiocyte development, after MEL1 and before PAIR1.
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Affiliation(s)
- Jakyung Yi
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
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206
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Tucker MR, Okada T, Hu Y, Scholefield A, Taylor JM, Koltunow AMG. Somatic small RNA pathways promote the mitotic events of megagametogenesis during female reproductive development in Arabidopsis. Development 2012; 139:1399-404. [PMID: 22399683 DOI: 10.1242/dev.075390] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Female gamete development in Arabidopsis ovules comprises two phases. During megasporogenesis, a somatic ovule cell differentiates into a megaspore mother cell and undergoes meiosis to produce four haploid megaspores, three of which degrade. The surviving functional megaspore participates in megagametogenesis, undergoing syncytial mitosis and cellular differentiation to produce a multicellular female gametophyte containing the egg and central cell, progenitors of the embryo and endosperm of the seed. The transition between megasporogenesis and megagametogenesis is poorly characterised, partly owing to the inaccessibility of reproductive cells within the ovule. Here, laser capture microdissection was used to identify genes expressed in and/or around developing megaspores during the transition to megagametogenesis. ARGONAUTE5 (AGO5), a putative effector of small RNA (sRNA) silencing pathways, was found to be expressed around reproductive cells during megasporogenesis, and a novel semi-dominant ago5-4 insertion allele showed defects in the initiation of megagametogenesis. Expression of a viral RNAi suppressor, P1/Hc-Pro, driven by the WUSCHEL and AGO5 promoters in somatic cells flanking the megaspores resulted in a similar phenotype. This indicates that sRNA-dependent pathways acting in somatic ovule tissues promote the initiation of megagametogenesis in the functional megaspore. Notably, these pathways are independent of AGO9, which functions in somatic epidermal ovule cells to inhibit the formation of multiple megaspore-like cells. Therefore, one somatic sRNA pathway involving AGO9 restricts reproductive development to the functional megaspore and a second pathway, inhibited by ago5-4 and P1/Hc-Pro, promotes megagametogenesis.
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Affiliation(s)
- Matthew R Tucker
- CSIRO Plant Industry, Waite Campus, Hartley Grove, Urrbrae, SA 5064, Australia
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207
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Zhou H, Liu Q, Li J, Jiang D, Zhou L, Wu P, Lu S, Li F, Zhu L, Liu Z, Chen L, Liu YG, Zhuang C. Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA. Cell Res 2012; 22:649-60. [PMID: 22349461 DOI: 10.1038/cr.2012.28] [Citation(s) in RCA: 198] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Photoperiod- and thermo-sensitive genic male sterility (PGMS and TGMS) are the core components for hybrid breeding in crops. Hybrid rice based on the two-line system using PGMS and TGMS lines has been successfully developed and applied widely in agriculture. However, the molecular mechanism underlying the control of PGMS and TGMS remains obscure. In this study, we mapped and cloned a major locus, p/tms12-1 (photo- or thermo-sensitive genic male sterility locus on chromosome 12), which confers PGMS in the japonica rice line Nongken 58S (NK58S) and TGMS in the indica rice line Peiai 64S (PA64S, derived from NK58S). A 2.4-kb DNA fragment containing the wild-type allele P/TMS12-1 was able to restore the pollen fertility of NK58S and PA64S plants in genetic complementation. P/TMS12-1 encodes a unique noncoding RNA, which produces a 21-nucleotide small RNA that we named osa-smR5864w. A substitution of C-to-G in p/tms12-1, the only polymorphism relative to P/TMS12-1, is present in the mutant small RNA, namely osa-smR5864m. Furthermore, overexpression of a 375-bp sequence of P/TMS12-1 in transgenic NK58S and PA64S plants also produced osa-smR5864w and restored pollen fertility. The small RNA was expressed preferentially in young panicles, but its expression was not markedly affected by different day lengths or temperatures. Our results reveal that the point mutation in p/tms12-1, which probably leads to a loss-of-function for osa-smR5864m, constitutes a common cause for PGMS and TGMS in the japonica and indica lines, respectively. Our findings thus suggest that this noncoding small RNA gene is an important regulator of male development controlled by cross-talk between the genetic networks and environmental conditions.
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Affiliation(s)
- Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
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208
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Migicovsky Z, Kovalchuk I. Epigenetic Modifications during Angiosperm Gametogenesis. FRONTIERS IN PLANT SCIENCE 2012; 3:20. [PMID: 22645573 PMCID: PMC3355800 DOI: 10.3389/fpls.2012.00020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Accepted: 01/19/2012] [Indexed: 06/01/2023]
Abstract
Angiosperms do not contain a distinct germline, but rather develop gametes from gametophyte initials that undergo cell division. These gametes contain cells that give rise to an endosperm and the embryo. DNA methylation is decreased in the vegetative nucleus (VN) and central cell nuclei (CCN) resulting in expression of transposable elements (TEs). It is thought that the siRNAs produced in response to TE expression are able to travel to the sperm cells and egg cells (EC) from VN and CCN, respectively, in order to enforce silencing there. Demethylation during gametogenesis helps ensure that even newly integrated TEs are expressed and therefore silenced by the resulting siRNA production. A final form of epigenetic control is modification of histones, which includes accumulation of the H3 variant HTR10 in mature sperm that is then completely replaced following fertilization. In females, the histone isoforms present in the EC and CCN differ, potentially helping to differentiate the two components during gametogenesis.
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Affiliation(s)
- Zoë Migicovsky
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
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209
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Hong L, Tang D, Zhu K, Wang K, Li M, Cheng Z. Somatic and reproductive cell development in rice anther is regulated by a putative glutaredoxin. THE PLANT CELL 2012; 24:577-88. [PMID: 22319054 PMCID: PMC3315234 DOI: 10.1105/tpc.111.093740] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The switch from mitosis to meiosis is one of the most pivotal events in eukaryotes undergoing sexual reproduction. However, the mechanisms orchestrating meiosis initiation remain elusive, particularly in plants. Flowering plants are heterosporous, with male and female spore genesis adopting different developmental courses. We show here that plant pollen mother cells contain a specific meiosis initiation machinery through characterization of a rice (Oryza sativa) gene, MICROSPORELESS1 (MIL1). The mil1 mutant does not produce microspores in anthers but has the normal female fertility. Detailed molecular and cytological investigations demonstrate that mil1 anthers are defective in the meiotic entry of sporogenous cell progenies and in the differentiation of surrounding somatic cell layers, resulting in locules filled with somatic cells instead of microspores. Furthermore, analysis of mil1 msp1 double mutants reveals that due to the absence of MIL1, the cells in their anther locule center do not activate meiotic cell cycle either, generating a similar anther phenotype to mil1. MIL1 encodes a plant-specific CC-type glutaredoxin, which could interact with TGA transcription factors. These results suggest meiotic entry in microsporocytes is directed by an anther-specific mechanism, which requires MIL1 activity, and redox regulation might play important roles in this process.
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210
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Comprehensive network analysis of anther-expressed genes in rice by the combination of 33 laser microdissection and 143 spatiotemporal microarrays. PLoS One 2011; 6:e26162. [PMID: 22046259 PMCID: PMC3202526 DOI: 10.1371/journal.pone.0026162] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 09/21/2011] [Indexed: 11/23/2022] Open
Abstract
Co-expression networks systematically constructed from large-scale transcriptome data reflect the interactions and functions of genes with similar expression patterns and are a powerful tool for the comprehensive understanding of biological events and mining of novel genes. In Arabidopsis (a model dicot plant), high-resolution co-expression networks have been constructed from very large microarray datasets and these are publicly available as online information resources. However, the available transcriptome data of rice (a model monocot plant) have been limited so far, making it difficult for rice researchers to achieve reliable co-expression analysis. In this study, we performed co-expression network analysis by using combined 44 K agilent microarray datasets of rice, which consisted of 33 laser microdissection (LM)-microarray datasets of anthers, and 143 spatiotemporal transcriptome datasets deposited in RicexPro. The entire data of the rice co-expression network, which was generated from the 176 microarray datasets by the Pearson correlation coefficient (PCC) method with the mutual rank (MR)-based cut-off, contained 24,258 genes and 60,441 genes pairs. Using these datasets, we constructed high-resolution co-expression subnetworks of two specific biological events in the anther, “meiosis” and “pollen wall synthesis”. The meiosis network contained many known or putative meiotic genes, including genes related to meiosis initiation and recombination. In the pollen wall synthesis network, several candidate genes involved in the sporopollenin biosynthesis pathway were efficiently identified. Hence, these two subnetworks are important demonstrations of the efficiency of co-expression network analysis in rice. Our co-expression analysis included the separated transcriptomes of pollen and tapetum cells in the anther, which are able to provide precise information on transcriptional regulation during male gametophyte development in rice. The co-expression network data presented here is a useful resource for rice researchers to elucidate important and complex biological events.
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211
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Van Ex F, Jacob Y, Martienssen RA. Multiple roles for small RNAs during plant reproduction. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:588-93. [PMID: 21807552 PMCID: PMC3389783 DOI: 10.1016/j.pbi.2011.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 07/10/2011] [Accepted: 07/11/2011] [Indexed: 05/05/2023]
Abstract
Germline development and early embryogenesis in eukaryotes are characterized by large-scale genome reprogramming events. In companion cells of the Arabidopsis male gametophyte, epigenome reorganization leads to loss of heterochromatin and production of a distinct small RNA (sRNA) population. A specific class of sRNA derived from transposons appears to be mobile and can accumulate in germ cells. In the germline of maize, rice, and Arabidopsis, specific ARGONAUTE-sRNA silencing complexes appear to play key roles in reproductive development, including meiosis and regulation of germ cell fate. These results reveal new roles for sRNAs during plant reproduction and suggest that mobility of sRNAs could be critical for some of these functions.
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Affiliation(s)
- Frédéric Van Ex
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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212
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Chevalier É, Loubert-Hudon A, Zimmerman EL, Matton DP. Cell-cell communication and signalling pathways within the ovule: from its inception to fertilization. THE NEW PHYTOLOGIST 2011; 192:13-28. [PMID: 21793830 DOI: 10.1111/j.1469-8137.2011.03836.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Cell-cell communication pervades every aspect of the life of a plant. It is particularly crucial for the development of the gametes and their subtle interaction leading to double fertilization. The ovule is composed of a funiculus, one or two integuments, and a gametophyte surrounded by nucellus tissue. Proper ovule and embryo sac development are critical to reproductive success. To allow fertilization, the correct relative positioning and differentiation of the embryo sac cells are essential. Integument development is also intimately linked with the normal development of the female gametophyte; the sporophyte and gametophyte are not fully independent tissues. Inside the gametophyte, numerous signs of cell-cell communication take place throughout development, including cell fate patterning, fertilization and the early stages of embryogenesis. This review highlights the current evidence of cell-cell communication and signalling elements based on structural and physiological observations as well as the description and characterization of mutants in structurally specific genes. By combining data from different species, models of cell-cell interactions have been built, particularly for the establishment of the germline, for the progression through megagametogenesis and for double fertilization.
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Affiliation(s)
- Éric Chevalier
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC, Canada H1X 2B2
| | - Audrey Loubert-Hudon
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC, Canada H1X 2B2
| | - Erin L Zimmerman
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC, Canada H1X 2B2
| | - Daniel P Matton
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 rue Sherbrooke est, Montréal, QC, Canada H1X 2B2
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213
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Abstract
In most eukaryotes, histone and DNA modifications are responsible for the silencing of genes integrated in heterochromatic sequences, as well as the silencing of pericentromeric repeats and transposable elements themselves. But the mechanisms that guide these modifications to heterochromatin during the cell cycle have been elusive. RNA interference takes advantage of heterochromatic transcription to process small RNAs and recruit enzymes required for both histone and DNA modifications, and is one such mechanism that has been identified. The processes are best understood in fission yeast and plants, but recent work in mammalian cells, especially in the germline, suggests these mechanisms may be highly conserved.
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Affiliation(s)
- Tom Volpe
- Department of Molecular and Cellular Biology, Northwestern University, Chicago, Illinois 60611, USA
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214
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Cloning plants by seeds: Inheritance models and candidate genes to increase fundamental knowledge for engineering apomixis in sexual crops. J Biotechnol 2011; 159:291-311. [PMID: 21906637 DOI: 10.1016/j.jbiotec.2011.08.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 08/16/2011] [Accepted: 08/17/2011] [Indexed: 01/02/2023]
Abstract
Apomixis is desirable in agriculture as a reproductive strategy for cloning plants by seeds. Because embryos derive from the parthenogenic development of apomeiotic egg cells, apomixis excludes fertilization in addition to meiotic segregation and recombination, resulting in offspring that are exact replicas of the parent. Introgression of apomixis from wild relatives to crop species and transformation of sexual genotypes into apomictically reproducing ones are long-held goals of plant breeding. In fact, it is generally accepted that the introduction of apomixis into agronomically important crops will have revolutionary implications for agriculture. This review deals with the current genetic and molecular findings that have been collected from model species to elucidate the mechanisms of apomeiosis, parthenogenesis and apomixis as a whole. Our goal is to critically determine whether biotechnology can combine key genes known to control the expression of the processes miming the main components of apomixis in plants. Two natural apomicts, as the eudicot Hypericum perforatum L. (St. John's wort) and the monocot Paspalum spp. (crowngrass), and the sexual model species Arabidopsis thaliana are ideally suited for such investigations at the genomic and biotechnological levels. Some novel views and original concepts have been faced on this review, including (i) the parallel between Y-chromosome and apomixis-bearing chromosome (e.g., comparative genomic analyses revealed common features as repression of recombination events, accumulation of transposable elements and degeneration of genes) from the most primitive (Hypericum-type) to the most advanced (Paspalum-type) in evolutionary terms, and (ii) the link between apomixis and gene-specific silencing mechanisms (i.e., likely based on chromatin remodelling factors), with merging lines of evidence regarding the role of auxin in cell fate specification of embryo sac and egg cell development in Arabidopsis. The production of engineered plants exhibiting apomictic-like phenotypes is critically reviewed and discussed.
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215
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Nan GL, Ronceret A, Wang RC, Fernandes JF, Cande WZ, Walbot V. Global transcriptome analysis of two ameiotic1 alleles in maize anthers: defining steps in meiotic entry and progression through prophase I. BMC PLANT BIOLOGY 2011; 11:120. [PMID: 21867558 PMCID: PMC3180651 DOI: 10.1186/1471-2229-11-120] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 08/26/2011] [Indexed: 05/21/2023]
Abstract
BACKGROUND Developmental cues to start meiosis occur late in plants. Ameiotic1 (Am1) encodes a plant-specific nuclear protein (AM1) required for meiotic entry and progression through early prophase I. Pollen mother cells (PMCs) remain mitotic in most am1 mutants including am1-489, while am1-praI permits meiotic entry but PMCs arrest at the leptotene/zygotene (L/Z) transition, defining the roles of AM1 protein in two distinct steps of meiosis. To gain more insights into the roles of AM1 in the transcriptional pre-meiotic and meiotic programs, we report here an in depth analysis of gene expression alterations in carefully staged anthers at 1 mm (meiotic entry) and 1.5 mm (L/Z) caused by each of these am1 alleles. RESULTS 1.0 mm and 1.5 mm anthers of am1-489 and am1-praI were profiled in comparison to fertile siblings on Agilent® 4 × 44 K microarrays. Both am1-489 and am1-praI anthers are cytologically normal at 1.0 mm and show moderate transcriptome alterations. At the 1.5-mm stage both mutants are aberrant cytologically, and show more drastic transcriptome changes. There are substantially more absolute On/Off and twice as many differentially expressed genes (sterile versus fertile) in am1-489 than in am1-praI. At 1.5 mm a total of 4,418 genes are up- or down-regulated in either am1-489 or am1-praI anthers. These are predominantly stage-specific transcripts. Many putative meiosis-related genes were found among them including a small subset of allele-specific, mis-regulated genes specific to the PMCs. Nearly 60% of transcriptome changes in the set of transcripts mis-regulated in both mutants (N = 530) are enriched in PMCs, and only 1% are enriched in the tapetal cell transcriptome. All array data reported herein will be deposited and accessible at MaizeGDB http://www.maizegdb.org/. CONCLUSIONS Our analysis of anther transcriptome modulations by two distinct am1 alleles, am1-489 and am1-praI, redefines the role of AM1 as a modulator of expression of a subset of meiotic genes, important for meiotic progression and provided stage-specific insights into the genetic networks associated with meiotic entry and early prophase I progression.
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Affiliation(s)
- Guo-Ling Nan
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Arnaud Ronceret
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Rachel C Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Institute of Plant and Microbial Biology (IPMB), Academia Sinica, Taipei, 11529, Taiwan
| | - John F Fernandes
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - W Zacheus Cande
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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216
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Zhang D, Luo X, Zhu L. Cytological analysis and genetic control of rice anther development. J Genet Genomics 2011; 38:379-90. [PMID: 21930097 DOI: 10.1016/j.jgg.2011.08.001] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 07/29/2011] [Accepted: 08/01/2011] [Indexed: 11/27/2022]
Abstract
Microsporogenesis and male gametogenesis are essential for the alternating life cycle of flowering plants between diploid sporophyte and haploid gametophyte generations. Rice (Oryza sativa) is the world's major staple food, and manipulation of pollen fertility is particularly important for the demands to increase rice grain yield. Towards a better understanding of the mechanisms controlling rice male reproductive development, we describe here the cytological changes of anther development through 14 stages, including cell division, differentiation and degeneration of somatic tissues consisting of four concentric cell layers surrounding and supporting reproductive cells as they form mature pollen grains through meiosis and mitosis. Furthermore, we compare the morphological difference of anthers and pollen grains in both monocot rice and eudicot Arabidopsis thaliana. Additionally, we describe the key genes identified to date critical for rice anther development and pollen formation.
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Affiliation(s)
- Dabing Zhang
- Institute of Plant Science, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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217
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Kimble J. Molecular regulation of the mitosis/meiosis decision in multicellular organisms. Cold Spring Harb Perspect Biol 2011; 3:a002683. [PMID: 21646377 PMCID: PMC3140684 DOI: 10.1101/cshperspect.a002683] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A major step in the journey from germline stem cell to differentiated gamete is the decision to leave the mitotic cell cycle and begin progression through the meiotic cell cycle. Over the past decade, molecular regulators of the mitosis/meiosis decision have been discovered in most of the major model multicellular organisms. Historically, the mitosis/meiosis decision has been closely linked with controls of germline self-renewal and the sperm/egg decision, especially in nematodes and mice. Molecular explanations of those linkages clarify our understanding of this fundamental germ cell decision, and unifying themes have begun to emerge. Although the complete circuitry of the decision is not known in any organism, the recent advances promise to impact key issues in human reproduction and agriculture.
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Affiliation(s)
- Judith Kimble
- Howard Hughes Medical Institute, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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218
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Du P, Wu J, Zhang J, Zhao S, Zheng H, Gao G, Wei L, Li Y. Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors. PLoS Pathog 2011; 7:e1002176. [PMID: 21901091 PMCID: PMC3161970 DOI: 10.1371/journal.ppat.1002176] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Accepted: 06/07/2011] [Indexed: 01/25/2023] Open
Abstract
RNA silencing, mediated by small RNAs including microRNAs (miRNAs) and small interfering RNAs (siRNAs), is a potent antiviral or antibacterial mechanism, besides regulating normal cellular gene expression critical for development and physiology. To gain insights into host small RNA metabolism under infections by different viruses, we used Solexa/Illumina deep sequencing to characterize the small RNA profiles of rice plants infected by two distinct viruses, Rice dwarf virus (RDV, dsRNA virus) and Rice stripe virus (RSV, a negative sense and ambisense RNA virus), respectively, as compared with those from non-infected plants. Our analyses showed that RSV infection enhanced the accumulation of some rice miRNA*s, but not their corresponding miRNAs, as well as accumulation of phased siRNAs from a particular precursor. Furthermore, RSV infection also induced the expression of novel miRNAs in a phased pattern from several conserved miRNA precursors. In comparison, no such changes in host small RNA expression was observed in RDV-infected rice plants. Significantly RSV infection elevated the expression levels of selective OsDCLs and OsAGOs, whereas RDV infection only affected the expression of certain OsRDRs. Our results provide a comparative analysis, via deep sequencing, of changes in the small RNA profiles and in the genes of RNA silencing machinery induced by different viruses in a natural and economically important crop host plant. They uncover new mechanisms and complexity of virus-host interactions that may have important implications for further studies on the evolution of cellular small RNA biogenesis that impact pathogen infection, pathogenesis, as well as organismal development.
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Affiliation(s)
- Peng Du
- Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Jianguo Wu
- Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jiayao Zhang
- School of Statistics, Renmin University of China, Beijing, China
| | - Shuqi Zhao
- Center for Bioinformatics, The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Hong Zheng
- Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Ge Gao
- Center for Bioinformatics, The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Liping Wei
- Center for Bioinformatics, The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Yi Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
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219
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Capitão C, Paiva JAP, Santos DM, Fevereiro P. In Medicago truncatula, water deficit modulates the transcript accumulation of components of small RNA pathways. BMC PLANT BIOLOGY 2011; 11:79. [PMID: 21569262 PMCID: PMC3098777 DOI: 10.1186/1471-2229-11-79] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 05/10/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND Small RNAs (sRNAs) are 20-24 nucleotide (nt) RNAs and are involved in plant development and response to abiotic stresses. Plants have several sRNA pathways implicated in the transcriptional and post-transcriptional silencing of gene expression. Two key enzyme families common to all pathways are the Dicer-like (DCL) proteins involved in sRNAs maturation and the Argonautes (AGOs) involved in the targeting and functional action of sRNAs. Post-transcriptional silencing mediated by AGOs may occur by cleavage or translational repression of target mRNA's, while transcriptional silencing may be controlled by DNA methylation and chromatin remodeling. Thus far, these gene families have not been characterized in legumes, nor has their involvement in adaptation to water deficit been studied. RESULTS A bioinformatic search in Medicago truncatula genome databases, using Arabidopsis thaliana AGO and DCL cDNA and protein sequences, identified three sequences encoding for putative Dicer-like genes and twelve sequences encoding for putative Argonaute genes. Under water deficit conditions and mainly in roots, MtDCL1 and MtAGO1, two enzymes probably involved in the processing and activation of microRNAs (miRNAs), increased their transcript levels. mir162 which target DCL1 mRNA and mir168 which target AGO1 mRNA reduced their expression in the roots of plants subjected to water deficit. Three putative genes, MtDCL3, MtAGO4b and MtAGO4c probably involved in DNA methylation mechanisms, increased their mRNA levels. However, the mRNA levels of MtAGO6 reduced, which probably encodes a protein with functions similar to MtAGO4. MtAGO7 mRNA levels increased and possibly encodes a protein involved in the production of trans-acting small interfering RNAs. The transcript abundance of MtAGO12a, MtAGO12b and MtAGO12c reduced under water deprivation. Plants recovered from water deprivation reacquire the mRNA levels of the controls. CONCLUSIONS Our work demonstrates that in M. truncatula the transcript accumulation of the components of small RNA pathways is being modulated under water deficit. This shows that the transcriptional and post-transcriptional control of gene expression mediated by sRNAs is probably involved in plant adaptation to abiotic environmental changes. In the future this will allow the manipulation of these pathways providing a more efficient response of legumes towards water shortage.
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Affiliation(s)
- Cláudio Capitão
- Laboratório de Biotecnologia de Células Vegetais, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Jorge AP Paiva
- Instituto de Investigação Científica e Tropical, Centro das Florestas e Produtos Florestais, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Dulce M Santos
- Instituto de Investigação Científica e Tropical, Centro de Veterinária e Zootecnia, Av. Universidade Técnica 1300-477 Lisboa, Portugal
| | - Pedro Fevereiro
- Laboratório de Biotecnologia de Células Vegetais, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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220
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Deveshwar P, Bovill WD, Sharma R, Able JA, Kapoor S. Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice. BMC PLANT BIOLOGY 2011; 11:78. [PMID: 21554676 PMCID: PMC3112077 DOI: 10.1186/1471-2229-11-78] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 05/09/2011] [Indexed: 05/17/2023]
Abstract
BACKGROUND In flowering plants, the anther is the site of male gametophyte development. Two major events in the development of the male germline are meiosis and the asymmetric division in the male gametophyte that gives rise to the vegetative and generative cells, and the following mitotic division in the generative cell that produces two sperm cells. Anther transcriptomes have been analyzed in many plant species at progressive stages of development by using microarray and sequence-by synthesis-technologies to identify genes that regulate anther development. Here we report a comprehensive analysis of rice anther transcriptomes at four distinct stages, focusing on identifying regulatory components that contribute to male meiosis and germline development. Further, these transcriptomes have been compared with the transcriptomes of 10 stages of rice vegetative and seed development to identify genes that express specifically during anther development. RESULTS Transcriptome profiling of four stages of anther development in rice including pre-meiotic (PMA), meiotic (MA), anthers at single-celled (SCP) and tri-nucleate pollen (TPA) revealed about 22,000 genes expressing in at least one of the anther developmental stages, with the highest number in MA (18,090) and the lowest (15,465) in TPA. Comparison of these transcriptome profiles to an in-house generated microarray-based transcriptomics database comprising of 10 stages/tissues of vegetative as well as reproductive development in rice resulted in the identification of 1,000 genes specifically expressed in anther stages. From this sub-set, 453 genes were specific to TPA, while 78 and 184 genes were expressed specifically in MA and SCP, respectively. The expression pattern of selected genes has been validated using real time PCR and in situ hybridizations. Gene ontology and pathway analysis of stage-specific genes revealed that those encoding transcription factors and components of protein folding, sorting and degradation pathway genes dominated in MA, whereas in TPA, those coding for cell structure and signal transduction components were in abundance. Interestingly, about 50% of the genes with anther-specific expression have not been annotated so far. CONCLUSIONS Not only have we provided the transcriptome constituents of four landmark stages of anther development in rice but we have also identified genes that express exclusively in these stages. It is likely that many of these candidates may therefore contribute to specific aspects of anther and/or male gametophyte development in rice. In addition, the gene sets that have been produced will assist the plant reproductive community in building a deeper understanding of underlying regulatory networks and in selecting gene candidates for functional validation.
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Affiliation(s)
- Priyanka Deveshwar
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi-110021, India
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221
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Le Trionnaire G, Grant-Downton RT, Kourmpetli S, Dickinson HG, Twell D. Small RNA activity and function in angiosperm gametophytes. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:1601-10. [PMID: 21172810 DOI: 10.1093/jxb/erq399] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Small non-coding RNAs are key post-transcriptional and transcriptional regulators of plant gene expression in angiosperm sporophytes. In recent years, gametophytic small RNAs have also been investigated, predominantly in Arabidopsis male gametophytes, revealing features in common with the sporophyte as well as some surprising differences. Transcriptomic and deep-sequencing studies confirm that multiple small RNA pathways operate in male gametophytes, with over 100 miRNAs detected throughout development. Trans-acting siRNA pathways that are associated with novel phased transcripts in pollen, and the nat-siRNA pathway have important roles in pollen maturation and gamete function. Moreover, a role for siRNA-triggered silencing of transposable elements in male and female germ cells has been established, a feature in common with the role of piRNAs in animal germlines. Current evidence supports an integral role for small RNAs in angiosperm gametophyte development and it can be anticipated that novel small RNAs with significant roles in germline development and genome integrity await discovery.
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Affiliation(s)
- G Le Trionnaire
- Department of Biology, University of Leicester, University Road, Leicester, UK
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222
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Borges F, Pereira PA, Slotkin RK, Martienssen RA, Becker JD. MicroRNA activity in the Arabidopsis male germline. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:1611-20. [PMID: 21357774 PMCID: PMC5536363 DOI: 10.1093/jxb/erq452] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 12/13/2010] [Accepted: 12/15/2010] [Indexed: 05/19/2023]
Abstract
Most of the core proteins involved in the microRNA (miRNA) pathway in plants have been identified, and almost simultaneously hundreds of miRNA sequences processed in the Arabidopsis sporophyte have been discovered by exploiting next-generation sequencing technologies. However, there is very limited understanding about potentially distinct mechanisms of post-transcriptional regulation between different cell lineages. In this review the focus is on the Arabidopsis male gametophyte (pollen), where the germline differentiates after meiosis giving rise to the male gametes. Based on comparative analysis of miRNAs identified in sperm cells by in-depth sequencing, their possible functions during germ cell specification and beyond fertilization are discussed. In addition, 25 potentially novel miRNAs processed in sperm cells and pollen were identified, as well as enriched variations in the sequence length of known miRNAs, which might indicate subfunctionalization by association with a putative germline-specific Argonaute complex. ARGONAUTE 5 (AGO5), by close homology to AGO1 and localizing preferentially to the sperm cell cytoplasm in mature pollen, may be part of such a complex.
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223
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Genome reprogramming and small interfering RNA in the Arabidopsis germline. Curr Opin Genet Dev 2011; 21:134-9. [PMID: 21330131 DOI: 10.1016/j.gde.2011.01.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 01/18/2011] [Indexed: 12/31/2022]
Abstract
The movement of mobile small RNA signals between cells has garnered much interest over the last few years, and has recently been extended to germ cells during gamete development. Focusing on plants, we review mobile RNA signals that arise following reprogramming in the germline, and their effect on transposable element silencing on the one hand and on meiotic and apomictic germ cell fate on the other. A potential role for reprogramming and small RNA in hybrid formation and speciation is proposed.
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224
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Baroux C, Raissig MT, Grossniklaus U. Epigenetic regulation and reprogramming during gamete formation in plants. Curr Opin Genet Dev 2011; 21:124-33. [PMID: 21324672 DOI: 10.1016/j.gde.2011.01.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 01/18/2011] [Indexed: 11/29/2022]
Abstract
Plants and animals reproduce sexually via specialized, highly differentiated gametes. Yet, gamete formation drastically differs between the two kingdoms. In flowering plants, the specification of cells destined to enter meiosis occurs late in development, gametic and accessory cells are usually derived from the same meiotic product, and two distinct female gametes involved in double fertilization differentiate. This poses fascinating questions in terms of gamete development and the associated epigenetic processes. Although studies in this area remain at their infancy, it becomes clear that large-scale epigenetic reprogramming, involving RNA-directed DNA methylation, chromatin modifications, and nucleosome remodeling, contributes to the establishment of transcriptionally repressive or permissive epigenetic landscapes. Furthermore, a role for small RNAs in the regulation of transposable elements during gametogenesis is emerging.
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Affiliation(s)
- Célia Baroux
- Institute of Plant Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland.
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225
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Singh M, Goel S, Meeley RB, Dantec C, Parrinello H, Michaud C, Leblanc O, Grimanelli D. Production of viable gametes without meiosis in maize deficient for an ARGONAUTE protein. THE PLANT CELL 2011; 23:443-58. [PMID: 21325139 PMCID: PMC3077773 DOI: 10.1105/tpc.110.079020] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 12/31/2010] [Accepted: 01/24/2011] [Indexed: 05/18/2023]
Abstract
Apomixis is a form of asexual reproduction through seeds in angiosperms. Apomictic plants bypass meiosis and fertilization, developing offspring that are genetically identical to their mother. In a genetic screen for maize (Zea mays) mutants mimicking aspects of apomixis, we identified a dominant mutation resulting in the formation of functional unreduced gametes. The mutant shows defects in chromatin condensation during meiosis and subsequent failure to segregate chromosomes. The mutated locus codes for AGO104, a member of the ARGONAUTE family of proteins. AGO104 accumulates specifically in somatic cells surrounding the female meiocyte, suggesting a mobile signal rather than cell-autonomous control. AGO104 is necessary for non-CG methylation of centromeric and knob-repeat DNA. Digital gene expression tag profiling experiments using high-throughput sequencing show that AGO104 influences the transcription of many targets in the ovaries, with a strong effect on centromeric repeats. AGO104 is related to Arabidopsis thaliana AGO9, but while AGO9 acts to repress germ cell fate in somatic tissues, AGO104 acts to repress somatic fate in germ cells. Our findings show that female germ cell development in maize is dependent upon conserved small RNA pathways acting non-cell-autonomously in the ovule. Interfering with this repression leads to apomixis-like phenotypes in maize.
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Affiliation(s)
- Manjit Singh
- Institut de Recherche pour le Développement, Plant Genome and Development Laboratory, UMR5096, 34394 Montpellier, France
| | - Shalendra Goel
- Institut de Recherche pour le Développement, Plant Genome and Development Laboratory, UMR5096, 34394 Montpellier, France
| | | | - Christelle Dantec
- Montpellier GenomiX, Institut de Génomique Fonctionelle, 34094 Montpellier, France
| | - Hugues Parrinello
- Montpellier GenomiX, Institut de Génomique Fonctionelle, 34094 Montpellier, France
| | - Caroline Michaud
- Institut de Recherche pour le Développement, Plant Genome and Development Laboratory, UMR5096, 34394 Montpellier, France
| | - Olivier Leblanc
- Institut de Recherche pour le Développement, Plant Genome and Development Laboratory, UMR5096, 34394 Montpellier, France
| | - Daniel Grimanelli
- Institut de Recherche pour le Développement, Plant Genome and Development Laboratory, UMR5096, 34394 Montpellier, France
- Address correspondence to
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226
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Sato Y, Antonio B, Namiki N, Motoyama R, Sugimoto K, Takehisa H, Minami H, Kamatsuki K, Kusaba M, Hirochika H, Nagamura Y. Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice. BMC PLANT BIOLOGY 2011; 11:10. [PMID: 21226959 PMCID: PMC3031230 DOI: 10.1186/1471-2229-11-10] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 01/12/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plant growth depends on synergistic interactions between internal and external signals, and yield potential of crops is a manifestation of how these complex factors interact, particularly at critical stages of development. As an initial step towards developing a systems-level understanding of the biological processes underlying the expression of overall agronomic potential in cereal crops, a high-resolution transcriptome analysis of rice was conducted throughout life cycle of rice grown under natural field conditions. RESULTS A wide range of gene expression profiles based on 48 organs and tissues at various developmental stages identified 731 organ/tissue specific genes as well as 215 growth stage-specific expressed genes universally in leaf blade, leaf sheath, and root. Continuous transcriptome profiling of leaf from transplanting until harvesting further elucidated the growth-stage specificity of gene expression and uncovered two major drastic changes in the leaf transcriptional program. The first major change occurred before the panicle differentiation, accompanied by the expression of RFT1, a putative florigen gene in long day conditions, and the downregulation of the precursors of two microRNAs. This transcriptome change was also associated with physiological alterations including phosphate-homeostasis state as evident from the behavior of several key regulators such as miR399. The second major transcriptome change occurred just after flowering, and based on analysis of sterile mutant lines, we further revealed that the formation of strong sink, i.e., a developing grain, is not the major cause but is rather a promoter of this change. CONCLUSIONS Our study provides not only the genetic basis for functional genomics in rice but also new insight into understanding the critical physiological processes involved in flowering and seed development, that could lead to novel strategies for optimizing crop productivity.
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Affiliation(s)
- Yutaka Sato
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Baltazar Antonio
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Nobukazu Namiki
- Mitsubishi Space Software Co. Ltd., Takezono 1-6-1, Tsukuba, Ibaraki 305-0032, Japan
| | - Ritsuko Motoyama
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Kazuhiko Sugimoto
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Hinako Takehisa
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroshi Minami
- Mitsubishi Space Software Co. Ltd., Takezono 1-6-1, Tsukuba, Ibaraki 305-0032, Japan
| | - Kaori Kamatsuki
- Mitsubishi Space Software Co. Ltd., Takezono 1-6-1, Tsukuba, Ibaraki 305-0032, Japan
| | - Makoto Kusaba
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Hirohiko Hirochika
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | - Yoshiaki Nagamura
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
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227
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Abstract
The events occurring at the onset of meiosis have not been fully elucidated. In the present study, OsAM1 was identified in rice (Oryza sativa L.) by map-based cloning. OsAM1, a homolog of Arabidopsis SWI1 and maize AM1, encodes a protein with a coiled-coil domain in its central region. In the Osam1 mutant, pollen mother cells are arrested at leptotene, showing that OsAM1 is required for the leptotene-zygotene transition. Immunocytological analysis revealed that OsAM1 exists as foci in early prophase I meiocytes. Very faint OsREC8 foci persisted in the Osam1 mutant, indicating that OsAM1 is not required for the initial meiotic recruitment of OsREC8. In the absence of OsAM1, many other critical meiotic components, including PAIR2, ZEP1 and OsMER3, could not be correctly installed onto chromosomes. In contrast, in pair2, Osmer3 and zep1 mutants, OsAM1 could be loaded normally, suggesting that OsAM1 plays a fundamental role in building the proper chromosome structure at the beginning of meiosis.
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228
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Nonomura KI, Eiguchi M, Nakano M, Takashima K, Komeda N, Fukuchi S, Miyazaki S, Miyao A, Hirochika H, Kurata N. A novel RNA-recognition-motif protein is required for premeiotic G1/S-phase transition in rice (Oryza sativa L.). PLoS Genet 2011; 7:e1001265. [PMID: 21253568 PMCID: PMC3017114 DOI: 10.1371/journal.pgen.1001265] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 12/02/2010] [Indexed: 12/15/2022] Open
Abstract
The molecular mechanism for meiotic entry remains largely elusive in flowering plants. Only Arabidopsis SWI1/DYAD and maize AM1, both of which are the coiled-coil protein, are known to be required for the initiation of plant meiosis. The mechanism underlying the synchrony of male meiosis, characteristic to flowering plants, has also been unclear in the plant kingdom. In other eukaryotes, RNA-recognition-motif (RRM) proteins are known to play essential roles in germ-cell development and meiosis progression. Rice MEL2 protein discovered in this study shows partial similarity with human proline-rich RRM protein, deleted in Azoospermia-Associated Protein1 (DAZAP1), though MEL2 also possesses ankyrin repeats and a RING finger motif. Expression analyses of several cell-cycle markers revealed that, in mel2 mutant anthers, most germ cells failed to enter premeiotic S-phase and meiosis, and a part escaped from the defect and underwent meiosis with a significant delay or continued mitotic cycles. Immunofluorescent detection revealed that T7 peptide-tagged MEL2 localized at cytoplasmic perinuclear region of germ cells during premeiotic interphase in transgenic rice plants. This study is the first report of the plant RRM protein, which is required for regulating the premeiotic G1/S-phase transition of male and female germ cells and also establishing synchrony of male meiosis. This study will contribute to elucidation of similarities and diversities in reproduction system between plants and other species. Meiosis is a pivotal event to produce haploid spores and gametes in all sexually reproducing species and is a fundamentally different type of cell cycle from mitosis. Thus, the molecular mechanisms to switch the cell cycle from mitosis to meiosis have been studied by many researchers. In yeast and metazoans, RNA-binding proteins are known to play important roles in the post-transcriptional regulation of genes implicated in the meiotic entry and meiosis. In contrast, in the plant kingdom, the mechanisms to control the meiotic entry have largely remained elusive. In this study, we discover a novel RNA-recognition-motif (RRM) protein in rice (Oryza sativa L.), designated MEL2, and demonstrate that MEL2 is required for the faithful transition of germ cells from mitosis to meiotic cell cycle. Rice MEL2 shows partial similarity with human DAZAP1, which is an RRM protein and relates to Azoospermia syndrome in human, while there are critical structural differences between germline-specific RRM proteins of mammals and plants. Our findings will lead the molecular-biological studies of plant meiotic entry to the next steps and will enable a comparison of the systems of meiotic entry between animals and plants.
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Affiliation(s)
- Ken-Ichi Nonomura
- Experimental Farm, National Institute of Genetics, Mishima, Shizuoka, Japan.
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229
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Zhou S, Wang Y, Li W, Zhao Z, Ren Y, Wang Y, Gu S, Lin Q, Wang D, Jiang L, Su N, Zhang X, Liu L, Cheng Z, Lei C, Wang J, Guo X, Wu F, Ikehashi H, Wang H, Wan J. Pollen semi-sterility1 encodes a kinesin-1-like protein important for male meiosis, anther dehiscence, and fertility in rice. THE PLANT CELL 2011; 23:111-29. [PMID: 21282525 PMCID: PMC3051251 DOI: 10.1105/tpc.109.073692] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 12/16/2010] [Accepted: 12/28/2010] [Indexed: 05/20/2023]
Abstract
In flowering plants, male meiosis produces four microspores, which develop into pollen grains and are released by anther dehiscence to pollinate female gametophytes. The molecular and cellular mechanisms regulating male meiosis in rice (Oryza sativa) remain poorly understood. Here, we describe a rice pollen semi-sterility1 (pss1) mutant, which displays reduced spikelet fertility (~40%) primarily caused by reduced pollen viability (~50% viable), and defective anther dehiscence. Map-based molecular cloning revealed that PSS1 encodes a kinesin-1-like protein. PSS1 is broadly expressed in various organs, with highest expression in panicles. Furthermore, PSS1 expression is significantly upregulated during anther development and peaks during male meiosis. The PSS1-green fluorescent protein fusion is predominantly localized in the cytoplasm of rice protoplasts. Substitution of a conserved Arg (Arg-289) to His in the PSS1 motor domain nearly abolishes its microtubule-stimulated ATPase activity. Consistent with this, lagging chromosomes and chromosomal bridges were found at anaphase I and anaphase II of male meiosis in the pss1 mutant. Together, our results suggest that PSS1 defines a novel member of the kinesin-1 family essential for male meiotic chromosomal dynamics, male gametogenesis, and anther dehiscence in rice.
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Affiliation(s)
- Shirong Zhou
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Wanchang Li
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhigang Zhao
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yulong Ren
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yong Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Suhai Gu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dan Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ling Jiang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Ning Su
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Linglong Liu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiulin Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fuqing Wu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hiroshi Ikehashi
- Department of Plant and Resources College of Bioresources, Nihon University, Fujisawa, Kanagawa 252-8510, Japan
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianmin Wan
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Abstract
The angiosperm female gametophyte is critical for plant reproduction. It contains the egg cell and central cell that become fertilized and give rise to the embryo and endosperm of the seed, respectively. Female gametophyte development begins early in ovule development with the formation of a diploid megaspore mother cell that undergoes meiosis. One resulting haploid megaspore then develops into the female gametophyte. Genetic and epigenetic processes mediate specification of megaspore mother cell identity and limit megaspore mother cell formation to a single cell per ovule. Auxin gradients influence female gametophyte polarity and a battery of transcription factors mediate female gametophyte cell specification and differentiation. The mature female gametophyte secretes peptides that guide the pollen tube to the embryo sac and contains protein complexes that prevent seed development before fertilization. Post-fertilization, the female gametophyte influences seed development through maternal-effect genes and by regulating parental contributions. Female gametophytes can form by an asexual process called gametophytic apomixis, which involves formation of a diploid female gametophyte and fertilization-independent development of the egg into the embryo. These functions collectively underscore the important role of the female gametophyte in seed and food production.
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Affiliation(s)
- Gary N. Drews
- Department of Biology, University of Utah, Salt Lake City, UT 84112
- Address correspondence to
| | - Anna M.G Koltunow
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Waite Campus, South Australia 5064, Australia
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231
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Abstract
The flowering plant germline is produced during the haploid gametophytic stage. Defining the germline is complicated by the extreme reduction of the male and female gametophytes, also referred to as pollen and embryo sac, respectively. Both male and female gamete progenitors are segregated by an asymmetric cell division, as is the case for the germline in animals. Genetic studies and access to the transcriptome of isolated gametes have provided a regulatory framework for the mechanisms that define the male germline. What specifies female germline identity remains unknown. Recent evidence indicates that an auxin gradient provides positional information and plays a role in defining the identity of the female gamete lineage. The animal germline is also marked by production of small RNAs, and recent evidence indicates that this trait might be shared with the plant gamete lineage.
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Affiliation(s)
- Frédéric Berger
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
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232
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Yamaki S, Nagato Y, Kurata N, Nonomura KI. Ovule is a lateral organ finally differentiated from the terminating floral meristem in rice. Dev Biol 2010; 351:208-16. [PMID: 21146515 DOI: 10.1016/j.ydbio.2010.12.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 12/01/2010] [Accepted: 12/02/2010] [Indexed: 01/21/2023]
Abstract
The floral meristem is the homeostatic source of floral organs in angiosperms. In rice, after stamen and carpel differentiation, the floral meristem is terminated and exhausted to produce an ovule. To elucidate underlying mechanisms controlling the continuous process from floral meristem termination to ovule formation, we investigated two rice mutants showing abnormalities in ovule formation. In the weak mutant of the lonely guy gene, responsible for cytokinin activation to maintain the floral meristem, ovule formation was abolished inside the normally developing carpel. The loss-of-function of the OsMADS13 gene, encoding a MADS-box transcription factor, resulted in the replacement of ovule with extra carpels. The in situ expression of tissue-specific markers in both mutants revealed that a lateral region of the terminating floral meristem adjacent to the site of carpel initiation exclusively differentiated the ovule and is apparently distinct from the remainder of the floral meristem, in contrast to previous assumptions. Our findings also suggest that primordial germ cells are initiated independently of ovule formation, but dependently on the presence of active cytokinin. We propose a novel pattern of ovule formation in angiosperms, in which the ovule is a lateral organ finally differentiated from the terminating floral meristem in rice.
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Affiliation(s)
- Shinichiro Yamaki
- Genetic Strain Research Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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233
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Fujita M, Horiuchi Y, Ueda Y, Mizuta Y, Kubo T, Yano K, Yamaki S, Tsuda K, Nagata T, Niihama M, Kato H, Kikuchi S, Hamada K, Mochizuki T, Ishimizu T, Iwai H, Tsutsumi N, Kurata N. Rice expression atlas in reproductive development. PLANT & CELL PHYSIOLOGY 2010; 51:2060-81. [PMID: 21062870 DOI: 10.1093/pcp/pcq165] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. A decrease in expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes which appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several cyclin-dependent kinases (CDKs), cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the most extensive and most comprehensive data set available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed.
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Affiliation(s)
- Masahiro Fujita
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540 Japan
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234
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Mallory A, Vaucheret H. Form, function, and regulation of ARGONAUTE proteins. THE PLANT CELL 2010. [PMID: 21183704 DOI: 10.1105/tpc.110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Both transcriptional (TGS) and posttranscriptional gene silencing (PTGS) are conserved eukaryotic gene regulatory mechanisms, integral for taming exogenous (viruses and bacteria) or endogenous (repetitive elements and transposons) invasive nucleic acids to minimize their impact on genome integrity and function. TGS and PTGS also are essential for controlling the expression of protein coding genes throughout development or in response to environmental stimuli. In plants and animals, at least one member of the conserved ARGONAUTE (AGO) protein family comprises the catalytic engine of the silencing complex, which is guided by sequence-specific small RNA to cognate RNA. In this review, we present general features of plant and animal AGO proteins and detail our knowledge on the 10 Arabidopsis thaliana AGOs.
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Affiliation(s)
- Allison Mallory
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique, 78026 Versailles Cedex, France.
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235
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Mallory A, Vaucheret H. Form, function, and regulation of ARGONAUTE proteins. THE PLANT CELL 2010; 22:3879-89. [PMID: 21183704 PMCID: PMC3027166 DOI: 10.1105/tpc.110.080671] [Citation(s) in RCA: 262] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 11/28/2010] [Accepted: 12/08/2010] [Indexed: 05/18/2023]
Abstract
Both transcriptional (TGS) and posttranscriptional gene silencing (PTGS) are conserved eukaryotic gene regulatory mechanisms, integral for taming exogenous (viruses and bacteria) or endogenous (repetitive elements and transposons) invasive nucleic acids to minimize their impact on genome integrity and function. TGS and PTGS also are essential for controlling the expression of protein coding genes throughout development or in response to environmental stimuli. In plants and animals, at least one member of the conserved ARGONAUTE (AGO) protein family comprises the catalytic engine of the silencing complex, which is guided by sequence-specific small RNA to cognate RNA. In this review, we present general features of plant and animal AGO proteins and detail our knowledge on the 10 Arabidopsis thaliana AGOs.
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Affiliation(s)
- Allison Mallory
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Institut National de la Recherche Agronomique, 78026 Versailles Cedex, France.
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236
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Tang X, Zhang ZY, Zhang WJ, Zhao XM, Li X, Zhang D, Liu QQ, Tang WH. Global gene profiling of laser-captured pollen mother cells indicates molecular pathways and gene subfamilies involved in rice meiosis. PLANT PHYSIOLOGY 2010; 154:1855-70. [PMID: 20959420 PMCID: PMC2996036 DOI: 10.1104/pp.110.161661] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 10/15/2010] [Indexed: 05/19/2023]
Abstract
Pollen mother cells (PMCs) represent a critical early stage in plant sexual reproduction in which the stage is set for male gamete formation. Understanding the global molecular genetics of this early meiotic stage has so far been limited to whole stamen or floret transcriptome studies, but since PMCs are a discrete population of cells in developmental synchrony, they provide the potential for precise transcriptome analysis and for enhancing our understanding of the transition to meiosis. As a step toward identifying the premeiotic transcriptome, we performed microarray analysis on a homogenous population of rice (Oryza sativa) PMCs isolated by laser microdissection and compared them with those of tricellular pollen and seedling. Known meiotic genes, including OsSPO11-1, PAIR1, PAIR2, PAIR3, OsDMC1, OsMEL1, OsRAD21-4, OsSDS, and ZEP1, all showed preferential expression in PMCs. The Kyoto Encyclopedia of Genes and Genomes pathways significantly enriched in PMC-preferential genes are DNA replication and repair pathways. Our genome-wide survey showed that, in the buildup to meiosis, PMCs accumulate the molecular machinery for meiosis at the mRNA level. We identified 1,158 PMC-preferential genes and suggested candidate genes and pathways involved in meiotic recombination and meiotic cell cycle control. Regarding the developmental context for meiosis, the DEF-like, AGL2-like, and AGL6-like subclades of MADS box transcription factors are PMC-preferentially expressed, the trans-zeatin type of cytokinin might be preferentially synthesized, and the gibberellin signaling pathway is likely active in PMCs. The ubiquitin-mediated proteolysis pathway is enriched in the 127 genes that are expressed in PMCs but not in tricellular pollen or seedling.
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Affiliation(s)
| | | | | | | | | | | | | | - Wei-Hua Tang
- National Key Laboratory of Plant Molecular Genetics (X.T., Z.-Y.Z., D.Z., W.-H.T.) and Key Laboratory of Synthetic Biology (X.L.), Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China (X.T., Q.-Q.L.); and Institute of Systems Biology, Shanghai University, Shanghai 200444, China (W.-J.Z., X.-M.Z.)
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237
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Abstract
Plant reproduction occurs through the production of gametes by a haploid generation, the gametophyte. Flowering plants have highly reduced male and female gametophytes, called pollen grains and embryo sacs, respectively, consisting of only a few cells. Gametophytes are critical for sexual reproduction, but detailed understanding of their development remains poor as compared to the diploid sporophyte. This article reviews recent progress in understanding the mechanisms underlying gametophytic development and function in flowering plants. The focus is on genes and molecules involved in the processes of initiation, growth, cell specification, and fertilization of the male and female gametophytes derived primarily from studies in model systems.
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Affiliation(s)
- Hong Ma
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Institute of Plant Biology, Fudan University, Shanghai, China
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238
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Twell D. Male gametogenesis and germline specification in flowering plants. ACTA ACUST UNITED AC 2010; 24:149-60. [PMID: 21103996 DOI: 10.1007/s00497-010-0157-5] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 11/07/2010] [Indexed: 12/15/2022]
Abstract
During angiosperm male gametophyte development, the male germline is segregated by an asymmetric cell division of the haploid microspore. This review encompasses recent advances in understanding the genetic and molecular mechanisms involved in generating the male germline from this pluripotent germline initial and in specifying the production of the twin sperm cells required for double fertilization. Genetic studies and access to the transcriptome of isolated gametes have enabled remarkable progress in understanding some of the key regulators that control and integrate germ cell cycle progression with germline specification, and an emerging regulatory model is presented. Rapid advances have also been made in understanding epigenetic regulation and small RNA pathways in the male gametophyte and germline that impact on genome integrity and gamete development, traits that are shared with animal germlines. The review concludes with a perspective of the outstanding issues and directions of future research that will further our understanding of germline specification and the gametophytic control of pollen development.
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Affiliation(s)
- David Twell
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK.
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239
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He Y, Wei Q, Ge J, Jiang A, Gan L, Song Z, Cai D. Genome duplication effects on pollen development and the interrelated physiological substances in tetraploid rice with polyploid meiosis stability. PLANTA 2010; 232:1219-28. [PMID: 20717831 DOI: 10.1007/s00425-010-1249-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 07/29/2010] [Indexed: 05/07/2023]
Abstract
The breeding of polyploid rice made no breakthrough for a long time because of low seed set. The discovery and application of polyploid meiosis stability (PMeS) material played a pivotal role in solving this problem. Our results indicated that genome duplication led to different outcomes in different rice cultivars in terms of pollen fertility, viability, and the accumulation of important physiological substances such as free proline and endogenous hormones. Pollen from the PMeS HN2026-4X lines showed a high fertility and viability similar to those of HN2026-2X (4X indicates tetraploid while 2X indicates the diploid), whereas both rates decreased dramatically in Balilla-4X. The results of pollen microstructure and ultrastructure investigations suggested that the pollen development pattern in HN2026-4X appeared normal at all stages, but a lot of changes were discovered in Balilla-4X. Stable meiosis, timely tapetum degradation, and normal mitochondria development were critical factors insuring the high frequency pollen fertility of PMeS rice. The free proline content increased markedly in HN2026-4X as compared to HN2026-2X, but it was decreased for Balilla-4X. Genome duplication effects on regulating endogenous hormones accumulation in pollen were evident, resulting in the clear difference between PMeS HN2026-4X and Balilla-4X. The accumulation of IAA, ZR, and GA in mature pollen distinguished HN2026-4X from Balilla-4X, which was linked to normal pollen development. In particular, the excessive accumulation of ABA at the meiosis stage may be correlated to disorganized meiosis in Balilla-4X. All the results provided unequivocal evidence that genome duplication played specific roles in the normal pollen development of PMeS HN2026-4X.
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Affiliation(s)
- Yuchi He
- Faculty of Life Science, Hubei University, Wuhan, People's Republic of China.
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240
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Garcia-Aguilar M, Michaud C, Leblanc O, Grimanelli D. Inactivation of a DNA methylation pathway in maize reproductive organs results in apomixis-like phenotypes. THE PLANT CELL 2010; 22:3249-67. [PMID: 21037104 PMCID: PMC2990141 DOI: 10.1105/tpc.109.072181] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 09/23/2010] [Accepted: 10/09/2010] [Indexed: 05/18/2023]
Abstract
Apomictic plants reproduce asexually through seeds by avoiding both meiosis and fertilization. Although apomixis is genetically regulated, its core genetic component(s) has not been determined yet. Using profiling experiments comparing sexual development in maize (Zea mays) to apomixis in maize-Tripsacum hybrids, we identified six loci that are specifically downregulated in ovules of apomictic plants. Four of them share strong homology with members of the RNA-directed DNA methylation pathway, which in Arabidopsis thaliana is involved in silencing via DNA methylation. Analyzing loss-of-function alleles for two maize DNA methyltransferase genes belonging to that subset, dmt102 and dmt103, which are downregulated in the ovules of apomictic plants and are homologous to the Arabidopsis CHROMOMETHYLASEs and DOMAINS REARRANGED METHYLTRANSFERASE families, revealed phenotypes reminiscent of apomictic development, including the production of unreduced gametes and formation of multiple embryo sacs in the ovule. Loss of DMT102 activity in ovules resulted in the establishment of a transcriptionally competent chromatin state in the archesporial tissue and in the egg cell that mimics the chromatin state found in apomicts. Interestingly, dmt102 and dmt103 expression in the ovule is found in a restricted domain in and around the germ cells, indicating that a DNA methylation pathway active during reproduction is essential for gametophyte development in maize and likely plays a critical role in the differentiation between apomictic and sexual reproduction.
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241
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Mahfouz MM. RNA-directed DNA methylation: mechanisms and functions. PLANT SIGNALING & BEHAVIOR 2010; 5:806-16. [PMID: 20421728 PMCID: PMC3115029 DOI: 10.4161/psb.5.7.11695] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 03/03/2010] [Indexed: 05/21/2023]
Abstract
Epigenetic RNA based gene silencing mechanisms play a major role in genome stability and control of gene expression. Transcriptional gene silencing via RNA-directed DNA methylation (RdDM) guides the epigenetic regulation of the genome in response to disease states, growth, developmental and stress signals. RdDM machinery is composed of proteins that produce and modify 24-nt- long siRNAs, recruit the RdDM complex to genomic targets, methylate DNA and remodel chromatin. The final DNA methylation pattern is determined by either DNA methyltransferase alone or by the combined action of DNA methyltransferases and demethylases. The dynamic interaction between RdDM and demethylases may render the plant epigenome plastic to growth, developmental, and environmental cues. The epigenome plasticity may allow the plant genome to assume many epigenomes and to have the right epigenome at the right time in response to intracellular or extracellular stimuli. This review discusses recent advances in RdDM research and considers future perspectives.
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Affiliation(s)
- Magdy M Mahfouz
- Center for Plant Stress Genomics & Technology, 4700 King Abdullah University of Science & Technology, Kingdom of Saudi Arabia.
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242
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Abstract
The various classes of small non-coding RNAs are a fundamentally important component of the transcriptome. These molecules have roles in many essential processes such as regulation of gene expression at the transcriptional and post-transcriptional levels, guidance of DNA methylation and defence against selfish replicators such as transposons. Their diversity and functions in the sporophytic generation of angiosperms is well explored compared with the gametophytic generation, where little is known about them. Recent progress in understanding their abundance, diversity and function in the gametophyte is reviewed.
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243
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He J, Gray J, Leisner S. A Pelargonium ARGONAUTE4 gene shows organ-specific expression and differences in RNA and protein levels. JOURNAL OF PLANT PHYSIOLOGY 2010; 167:319-25. [PMID: 19879665 DOI: 10.1016/j.jplph.2009.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 10/03/2009] [Accepted: 10/03/2009] [Indexed: 05/13/2023]
Abstract
RNAi-induced gene silencing plays a role in plant DNA methylation and defense. While most gene silencing studies have been performed on annuals, little is known about the expression of key components of this process (like ARGONAUTE proteins) in ornamentals. Using a combination of polymerase chain reaction techniques, an ARGONAUTE4 gene, PhAGO4, was isolated from Pelargonium. PhAGO4 encodes a predicted product of 934 amino acids that contains the PAZ and PIWI domains typical of ARGONAUTE (AGO) proteins. Phylogenetic analyses indicate that PhAGO4 clusters with other plant AGO4 proteins. Organ expression patterns of the AGO4 genes in Pelargonium and Arabidopsis show intriguing differences. AGO4 RNA levels decline with leaf age in both Arabidopsis and Pelargonium. In contrast AGO4 RNA levels in roots relative to leaves are higher in Pelargonium than in Arabidopsis. Both Arabidopsis and Pelargonium AGO4 showed higher RNA levels in flowers than leaves or roots. Even though flowers show higher levels of PhAGO4 RNA when compared to leaves and roots, protein gel blot analysis shows that at the protein level, the reverse is true. This suggests that PhAGO4 expression may be regulated at the translational or post-translational level in Pelargonium flowers.
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Affiliation(s)
- Jie He
- Department of Biological Sciences, The University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
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Yu B, Wang H. Translational Inhibition by MicroRNAs in Plants. MIRNA REGULATION OF THE TRANSLATIONAL MACHINERY 2010; 50:41-57. [DOI: 10.1007/978-3-642-03103-8_3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Abstract
The extant land plants are unique among the monophyletic clade of photosynthetic eukaryotes, which consists of the green algae (chlorophytes), the charophycean algae (charophytes), numerous groups of unicellular algae (prasinophytes) and the embryophytes, by possessing, firstly, a sexual life cycle characterized by an alternation between a haploid, gametophytic and a diploid, sporophytic multicellular generation; secondly, the formation of egg cells within multicellular structures called archegonia; and, thirdly, the retention of the zygote and diploid sporophyte embryo within the archegonium. We review the developmental, paleobotanical and molecular evidence indicating that: the embryophytes descended from a charophyte-like ancestor; this common ancestor had a life cycle with only a haploid multicellular generation; and the most ancient (c. 410 Myr old) land plants (e.g. Cooksonia, Rhynia and Zosterophyllum) had a dimorphic life cycle (i.e. their haploid and diploid generations were morphologically different). On the basis of these findings, we suggest that the multicellular reproductive structures of extant charophytes and embryophytes are developmentally homologous, and that those of the embryophytes evolved by virtue of the co-option and re-deployment of ancient algal homeodomain gene networks.
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Affiliation(s)
- Karl J Niklas
- Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA.
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Yang WC, Shi DQ, Chen YH. Female gametophyte development in flowering plants. ANNUAL REVIEW OF PLANT BIOLOGY 2010; 61:89-108. [PMID: 20192738 DOI: 10.1146/annurev-arplant-042809-112203] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The multicellular female gametophyte, a unique feature of higher plants, provides us with an excellent experimental system to address fundamental questions in biology. During the past few years, we have gained significant insight into the mechanisms that control embryo sac polarity, gametophytic cell specification, and recognition between male and female gametophytic cells. An auxin gradient has been shown for the first time to function in the female gametophyte to regulate gametic cell fate, and key genes that control gametic cell fate have also been identified. This review provides an overview of these exciting discoveries with a focus on molecular and genetic data.
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Affiliation(s)
- Wei-Cai Yang
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
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Wu L, Zhang Q, Zhou H, Ni F, Wu X, Qi Y. Rice MicroRNA effector complexes and targets. THE PLANT CELL 2009; 21:3421-35. [PMID: 19903869 PMCID: PMC2798332 DOI: 10.1105/tpc.109.070938] [Citation(s) in RCA: 242] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Revised: 10/06/2009] [Accepted: 10/20/2009] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are small silencing RNAs with regulatory roles in gene expression. miRNAs interact with Argonaute (AGO) proteins to form effector complexes that cleave target mRNAs or repress translation. Rice (Oryza sativa) encodes four AGO1 homologs (AGO1a, AGO1b, AGO1c, and AGO1d). We used RNA interference (RNAi) to knock down the four AGO1s. The RNAi lines displayed pleiotropic developmental phenotypes and had increased accumulation of miRNA targets. AGO1a, AGO1b, and AGO1c complexes were purified and further characterized. The three AGO1s all have a strong preference for binding small RNAs (sRNAs) with 5' U and have Slicer activity. We cataloged the sRNAs in each AGO1 complex by deep sequencing and found that all three AGO1s predominantly bound known miRNAs. Most of the miRNAs were evenly distributed in the three AGO1 complexes, suggesting a redundant role for the AGO1s. Intriguingly, a subset of miRNAs were specifically incorporated into or excluded from one of the AGO1s, suggesting functional specialization among the AGO1s. Furthermore, we identified rice miRNA targets at a global level. The validated targets include transcription factors that control major stages of development and also genes involved in a variety of physiological processes, indicating a broad regulatory role for miRNAs in rice.
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Affiliation(s)
- Liang Wu
- National Institute of Biological Sciences, Beijing 102206, China
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Qingqing Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Huanyu Zhou
- National Institute of Biological Sciences, Beijing 102206, China
| | - Fangrui Ni
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xueying Wu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yijun Qi
- National Institute of Biological Sciences, Beijing 102206, China
- Address correspondence to
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Dickinson HG, Grant-Downton R. Bridging the generation gap: flowering plant gametophytes and animal germlines reveal unexpected similarities. Biol Rev Camb Philos Soc 2009; 84:589-615. [DOI: 10.1111/j.1469-185x.2009.00088.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Zheng L, Huang F, Narsai R, Wu J, Giraud E, He F, Cheng L, Wang F, Wu P, Whelan J, Shou H. Physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings. PLANT PHYSIOLOGY 2009; 151:262-74. [PMID: 19605549 PMCID: PMC2735995 DOI: 10.1104/pp.109.141051] [Citation(s) in RCA: 186] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Accepted: 07/08/2009] [Indexed: 05/18/2023]
Abstract
The antagonistic interaction between iron (Fe) and phosphorus (P) has been noted in the area of plant nutrition. To understand the physiology and molecular mechanisms of this interaction, we studied the growth performance, nutrient concentration, and gene expression profiles of root and shoot segments derived from 10-d-old rice (Oryza sativa) seedlings under four different nutrient conditions: (1) full strength of Fe and P (+Fe+P); (2) full strength of P and no Fe (-Fe+P); (3) full strength of Fe and no P (+Fe-P); and (4) without both Fe and P (-Fe-P). While removal of Fe in the growth medium resulted in very low shoot and root Fe concentrations, the chlorotic symptoms and retarded seedling growth were only observed on seedlings grown in the presence of P. Microarray data showed that in roots, 7,628 transcripts were significantly changed in abundance in the absence of Fe alone. Interestingly, many of these changes were reversed if P was also absent (-Fe-P), with only approximately 15% overlapping with -Fe alone (-Fe+P). Analysis of the soluble Fe concentration in rice seedling shoots showed that P deficiency resulted in significantly increased Fe availability within the plants. The soluble Fe concentration under -Fe-P conditions was similar to that under +Fe+P conditions. These results provide evidence that the presence of P can affect Fe availability and in turn can influence the regulation of Fe-responsive genes.
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Affiliation(s)
- Luqing Zheng
- Joint Research Laboratory in Genomics and Nutriomics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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