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Xu R, Chong L, Zhu Y. Mediator kinase subunit CDK8 phosphorylates transcription factor TCP15 during tomato pollen development. PLANT PHYSIOLOGY 2024; 195:865-878. [PMID: 38365204 DOI: 10.1093/plphys/kiae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/28/2023] [Accepted: 12/19/2023] [Indexed: 02/18/2024]
Abstract
Pollen development in flowering plants has strong implications for reproductive success. Pollen DNA can be targeted to improve plant traits for yield and stress tolerance. In this study, we demonstrated that the Mediator subunit CYCLIN-DEPENDENT KINASE 8 (CDK8) is a key modulator of pollen development in tomato (Solanum lycopersicum). SlCDK8 knockout led to significant decreases in pollen viability, fruit yield, and fruit seed number. We also found that SlCDK8 directly interacts with transcription factor TEOSINTE BRANCHED1-CYCLOIDEA-PCF15 (SlTCP15) using yeast two-hybrid screens. We subsequently showed that SlCDK8 phosphorylates Ser 187 of SlTCP15 to promote SlTCP15 stability. Phosphorylated TCP15 directly bound to the TGGGCY sequence in the promoters of DYSFUNCTIONAL TAPETUM 1 (SlDYT1) and MYB DOMAIN PROTEIN 103 (SlMYB103), which are responsible for pollen development. Consistently, disruption of SlTCP15 resembled slcdk8 tomato mutants. In sum, our work identified a new substrate of Mediator CDK8 and revealed an important regulatory role of SlCDK8 in pollen development via cooperation with SlTCP15.
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Affiliation(s)
- Rui Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Leelyn Chong
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China
- Sanya Institute of Henan University, Sanya, Hainan 570203, China
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2
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Wibowo AT, Antunez-Sanchez J, Dawson A, Price J, Meehan C, Wrightsman T, Collenberg M, Bezrukov I, Becker C, Benhamed M, Weigel D, Gutierrez-Marcos J. Predictable and stable epimutations induced during clonal plant propagation with embryonic transcription factor. PLoS Genet 2022; 18:e1010479. [PMID: 36383565 PMCID: PMC9731469 DOI: 10.1371/journal.pgen.1010479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/08/2022] [Accepted: 10/15/2022] [Indexed: 11/17/2022] Open
Abstract
Clonal propagation is frequently used in commercial plant breeding and biotechnology programs because it minimizes genetic variation, yet it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal variation. Several studies have linked epigenetic modifications induced during regeneration with this newly acquired phenotypic variation. However, the factors that determine the extent of somaclonal variation and the molecular changes underpinning this process remain poorly understood. To address this gap in our knowledge, we compared clonally propagated Arabidopsis thaliana plants derived from somatic embryogenesis using two different embryonic transcription factors- RWP-RK DOMAIN-CONTAINING 4 (RKD4) or LEAFY COTYLEDON2 (LEC2) and from two epigenetically distinct founder tissues. We found that both the epi(genetic) status of the explant and the regeneration protocol employed play critical roles in shaping the molecular and phenotypic landscape of clonal plants. Phenotypic variation in regenerated plants can be largely explained by the inheritance of tissue-specific DNA methylation imprints, which are associated with specific transcriptional and metabolic changes in sexual progeny of clonal plants. For instance, regenerants were particularly affected by the inheritance of root-specific epigenetic imprints, which were associated with an increased accumulation of salicylic acid in leaves and accelerated plant senescence. Collectively, our data reveal specific pathways underpinning the phenotypic and molecular variation that arise and accumulate in clonal plant populations.
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Affiliation(s)
- Anjar Tri Wibowo
- School of Life Science, University of Warwick, Coventry, United Kingdom
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
- Department of Biology, Faculty of Science and Technology, Airlangga University, Surabaya City, East Java, Indonesia
| | | | - Alexander Dawson
- School of Life Science, University of Warwick, Coventry, United Kingdom
| | - Jonathan Price
- School of Life Science, University of Warwick, Coventry, United Kingdom
| | - Cathal Meehan
- School of Life Science, University of Warwick, Coventry, United Kingdom
| | - Travis Wrightsman
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
| | - Maximillian Collenberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
| | - Ilja Bezrukov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
- Ludwig-Maximilians-University of Munich, Faculty of Biology, Biocenter, Martinsried, Germany
| | - Moussa Benhamed
- Université Paris-Saclay, Centre National de la Recherche Scientifique, Institut National De La Recherche Agronomique, University of Évry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
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3
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Sablowski R, Gutierrez C. Cycling in a crowd: Coordination of plant cell division, growth, and cell fate. THE PLANT CELL 2022; 34:193-208. [PMID: 34498091 PMCID: PMC8774096 DOI: 10.1093/plcell/koab222] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/31/2021] [Indexed: 05/25/2023]
Abstract
The reiterative organogenesis that drives plant growth relies on the constant production of new cells, which remain encased by interconnected cell walls. For these reasons, plant morphogenesis strictly depends on the rate and orientation of both cell division and cell growth. Important progress has been made in recent years in understanding how cell cycle progression and the orientation of cell divisions are coordinated with cell and organ growth and with the acquisition of specialized cell fates. We review basic concepts and players in plant cell cycle and division, and then focus on their links to growth-related cues, such as metabolic state, cell size, cell geometry, and cell mechanics, and on how cell cycle progression and cell division are linked to specific cell fates. The retinoblastoma pathway has emerged as a major player in the coordination of the cell cycle with both growth and cell identity, while microtubule dynamics are central in the coordination of oriented cell divisions. Future challenges include clarifying feedbacks between growth and cell cycle progression, revealing the molecular basis of cell division orientation in response to mechanical and chemical signals, and probing the links between cell fate changes and chromatin dynamics during the cell cycle.
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Affiliation(s)
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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4
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Mackenzie SA, Kundariya H. Organellar protein multi-functionality and phenotypic plasticity in plants. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190182. [PMID: 31787051 PMCID: PMC6939364 DOI: 10.1098/rstb.2019.0182] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
With the increasing impact of climate instability on agricultural and ecological systems has come a heightened sense of urgency to understand plant adaptation mechanisms in more detail. Plant species have a remarkable ability to disperse their progeny to a wide range of environments, demonstrating extraordinary resiliency mechanisms that incorporate epigenetics and transgenerational stability. Surprisingly, some of the underlying versatility of plants to adapt to abiotic and biotic stress emerges from the neofunctionalization of organelles and organellar proteins. We describe evidence of possible plastid specialization and multi-functional organellar protein features that serve to enhance plant phenotypic plasticity. These features appear to rely on, for example, spatio-temporal regulation of plastid composition, and unusual interorganellar protein targeting and retrograde signalling features that facilitate multi-functionalization. Although we report in detail on three such specializations, involving MSH1, WHIRLY1 and CUE1 proteins in Arabidopsis, there is ample reason to believe that these represent only a fraction of what is yet to be discovered as we begin to elaborate cross-species diversity. Recent observations suggest that plant proteins previously defined in one context may soon be rediscovered in new roles and that much more detailed investigation of proteins that show subcellular multi-targeting may be warranted. This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.
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Affiliation(s)
- Sally A Mackenzie
- Departments of Biology and Plant Science, The Pennsylvania State University, 362 Frear North Building, University Park, PA 16802, USA
| | - Hardik Kundariya
- Departments of Biology and Plant Science, The Pennsylvania State University, 362 Frear North Building, University Park, PA 16802, USA
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5
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Li H, Guo J, Zhang C, Zheng W, Song Y, Wang Y. Identification of Differentially Expressed miRNAs between a Wheat K-type Cytoplasmic Male Sterility Line and Its Near-Isogenic Restorer Line. PLANT & CELL PHYSIOLOGY 2019; 60:1604-1618. [PMID: 31076750 DOI: 10.1093/pcp/pcz065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
K-type cytoplasmic male sterility (KCMS) lines were ideal material for three-line hybrid wheat system due to the major role in hybrid wheat production. In this study, the morphology of developing microspore and mature pollen was compared between a KCMS line and its near-isogenic restorer line (KCMS-NIL). The most striking difference is that the microspore was unable to develop into tricellular pollen in the KCMS line. MicroRNA plays vital roles in flowering and gametophyte development. Small RNA sequencing identified a total of 274 known and 401 novel miRNAs differentially expressed between two lines or two developmental stages. Most of miRNAs with high abundance were differentially expressed at the uninucleate stage, and their expression level recovered or remained at the binucleate stage. Further degradome sequencing identified target genes which were mainly enriched in transcription regulation, phytohormone signaling and RNA degradation pathways. Combining with the transcriptome data, a correlation was found between the abnormal anther development, such as postmeiotic mitosis cessation, deformative pollen wall and the chromosome condensation of the vegetative cell, and the alterations in the related miRNA and their targets expression profiles. According to the correlation and pathway analysis, we propose a hypothetic miRNA-mediated network for the control of KCMS restoration.
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Affiliation(s)
- Hongxia Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jinglei Guo
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Chengyang Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Weijun Zheng
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Yulong Song
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Yu Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
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6
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Tedeschi F, Rizzo P, Huong BTM, Czihal A, Rutten T, Altschmied L, Scharfenberg S, Grosse I, Becker C, Weigel D, Bäumlein H, Kuhlmann M. EFFECTOR OF TRANSCRIPTION factors are novel plant-specific regulators associated with genomic DNA methylation in Arabidopsis. THE NEW PHYTOLOGIST 2019; 221:261-278. [PMID: 30252137 PMCID: PMC6585611 DOI: 10.1111/nph.15439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/01/2018] [Indexed: 05/02/2023]
Abstract
Plant-specific EFFECTORS OF TRANSCRIPTION (ET) are characterised by a variable number of highly conserved ET repeats, which are involved in zinc and DNA binding. In addition, ETs share a GIY-YIG domain, involved in DNA nicking activity. It was hypothesised that ETs might act as epigenetic regulators. Here, methylome, transcriptome and phenotypic analyses were performed to investigate the role of ET factors and their involvement in DNA methylation in Arabidopsis thaliana. Comparative DNA methylation and transcriptome analyses in flowers and seedlings of et mutants revealed ET-specific differentially expressed genes and mostly independently characteristic, ET-specific differentially methylated regions. Loss of ET function results in pleiotropic developmental defects. The accumulation of cyclobutane pyrimidine dimers after ultraviolet stress in et mutants suggests an ET function in DNA repair.
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Affiliation(s)
- Francesca Tedeschi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | - Paride Rizzo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | - Bui Thi Mai Huong
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | - Andreas Czihal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | | | - Ivo Grosse
- Department of BioinformaticsMartin‐Luther‐University06120HalleGermany
| | - Claude Becker
- Department of Molecular BiologyMax Planck Institute for Developmental Biology72076TübingenGermany
- Gregor Mendel Institute of Molecular Plant Biology1030ViennaAustria
| | - Detlef Weigel
- Department of Molecular BiologyMax Planck Institute for Developmental Biology72076TübingenGermany
| | - Helmut Bäumlein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466Seeland OT GaterslebenGermany
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Abstract
In the last decade, the accumulation and roles of small RNAs have been slowly uncovered. Recently, the RNA silencing pathways active in the male gametophyte of plants have started to be analyzed in depth. Although several studies have shed light on the small RNA populations present in the pollen, we still lack a clear picture of their regulatory activity. This chapter outlines an extraction method of mature pollen grains and its different downstream applications for the purification and detection of small RNAs.
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Affiliation(s)
- German Martinez
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, 750 07, Uppsala, Sweden.
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8
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Wibowo A, Becker C, Marconi G, Durr J, Price J, Hagmann J, Papareddy R, Putra H, Kageyama J, Becker J, Weigel D, Gutierrez-Marcos J. Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity. eLife 2016; 5:13546. [PMID: 27242129 PMCID: PMC4887212 DOI: 10.7554/elife.13546] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/25/2016] [Indexed: 12/31/2022] Open
Abstract
Inducible epigenetic changes in eukaryotes are believed to enable rapid adaptation to environmental fluctuations. We have found distinct regions of the Arabidopsis genome that are susceptible to DNA (de)methylation in response to hyperosmotic stress. The stress-induced epigenetic changes are associated with conditionally heritable adaptive phenotypic stress responses. However, these stress responses are primarily transmitted to the next generation through the female lineage due to widespread DNA glycosylase activity in the male germline, and extensively reset in the absence of stress. Using the CNI1/ATL31 locus as an example, we demonstrate that epigenetically targeted sequences function as distantly-acting control elements of antisense long non-coding RNAs, which in turn regulate targeted gene expression in response to stress. Collectively, our findings reveal that plants use a highly dynamic maternal 'short-term stress memory' with which to respond to adverse external conditions. This transient memory relies on the DNA methylation machinery and associated transcriptional changes to extend the phenotypic plasticity accessible to the immediate offspring.
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Affiliation(s)
- Anjar Wibowo
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Gianpiero Marconi
- School of Life Sciences, University of Warwick, Coventry, United Kingdom.,Department of Agricultural, Food and Environmental Science, University of Perugia, Perugia, Italy
| | - Julius Durr
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jonathan Price
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jorg Hagmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ranjith Papareddy
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Hadi Putra
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jorge Kageyama
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jorg Becker
- Instituto Gulbenkian de Ciencia, Oeiras, Portugal
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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9
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Bokszczanin KL, Krezdorn N, Fragkostefanakis S, Müller S, Rycak L, Chen Y, Hoffmeier K, Kreutz J, Paupière MJ, Chaturvedi P, Iannacone R, Müller F, Bostan H, Chiusano ML, Scharf KD, Rotter B, Schleiff E, Winter P. Identification of novel small ncRNAs in pollen of tomato. BMC Genomics 2015; 16:714. [PMID: 26385469 PMCID: PMC4575465 DOI: 10.1186/s12864-015-1901-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 09/09/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The unprecedented role of sncRNAs in the regulation of pollen biogenesis on both transcriptional and epigenetic levels has been experimentally proven. However, little is known about their global regulation, especially under stress conditions. We used tomato pollen in order to identify pollen stage-specific sncRNAs and their target mRNAs. We further deployed elevated temperatures to discern stress responsive sncRNAs. For this purpose high throughput sncRNA-sequencing as well as Massive Analysis of cDNA Ends (MACE) were performed for three-replicated sncRNAs libraries derived from tomato tetrad, post-meiotic, and mature pollen under control and heat stress conditions. RESULTS Using the omiRas analysis pipeline we identified known and predicted novel miRNAs as well as sncRNAs from other classes, responsive or not to heat. Differential expression analysis revealed that post-meiotic and mature pollen react most strongly by regulation of the expression of coding and non-coding genomic regions in response to heat. To gain insight to the function of these miRNAs, we predicted targets and annotated them to Gene Ontology terms. This approach revealed that most of them belong to protein binding, transcription, and Serine/Threonine kinase activity GO categories. Beside miRNAs, we observed differential expression of both tRNAs and snoRNAs in tetrad, post-meiotic, and mature pollen when comparing normal and heat stress conditions. CONCLUSIONS Thus, we describe a global spectrum of sncRNAs expressed in pollen as well as unveiled those which are regulated at specific time-points during pollen biogenesis. We integrated the small RNAs into the regulatory network of tomato heat stress response in pollen.
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Affiliation(s)
| | | | - Sotirios Fragkostefanakis
- Cluster of Excellence Frankfurt, Centre of Membrane Proteomics, Department of Biosciences, Goethe University, Frankfurt am Main, Germany
| | | | | | | | | | | | - Marine J Paupière
- Department of Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Palak Chaturvedi
- Department for Molecular Systems Biology, University of Vienna, Vienna, Austria
| | - Rina Iannacone
- ALSIA Research Center Metapontum Agrobios Metaponto (MT), Metaponto, Italy
| | - Florian Müller
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Hamed Bostan
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Klaus-Dieter Scharf
- Cluster of Excellence Frankfurt, Centre of Membrane Proteomics, Department of Biosciences, Goethe University, Frankfurt am Main, Germany
| | | | - Enrico Schleiff
- Cluster of Excellence Frankfurt, Centre of Membrane Proteomics, Department of Biosciences, Goethe University, Frankfurt am Main, Germany
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10
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Borg M, Berger F. Chromatin remodelling during male gametophyte development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:177-188. [PMID: 25892182 DOI: 10.1111/tpj.12856] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/10/2015] [Accepted: 04/14/2015] [Indexed: 05/28/2023]
Abstract
The plant life cycle alternates between a diploid sporophytic phase and haploid gametophytic phase, with the latter giving rise to the gametes. Male gametophyte development encompasses two mitotic divisions that results in a simple three-celled structure knows as the pollen grain, in which two sperm cells are encased within a larger vegetative cell. Both cell types exhibit a very different type of chromatin organization - highly condensed in sperm cell nuclei and highly diffuse in the vegetative cell. Distinct classes of histone variants have dynamic and differential expression in the two cell lineages of the male gametophyte. Here we review how the dynamics of histone variants are linked to reprogramming of chromatin activities in the male gametophyte, compaction of the sperm cell genome and zygotic transitions post-fertilization.
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Affiliation(s)
- Michael Borg
- Gregor Mendel Institute, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
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11
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Li Y, Córdoba-Cañero D, Qian W, Zhu X, Tang K, Zhang H, Ariza RR, Roldán-Arjona T, Zhu JK. An AP endonuclease functions in active DNA demethylation and gene imprinting in Arabidopsis [corrected]. PLoS Genet 2015; 11:e1004905. [PMID: 25569774 PMCID: PMC4287435 DOI: 10.1371/journal.pgen.1004905] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 11/18/2014] [Indexed: 11/19/2022] Open
Abstract
Active DNA demethylation in plants occurs through base excision repair, beginning with removal of methylated cytosine by the ROS1/DME subfamily of 5-methylcytosine DNA glycosylases. Active DNA demethylation in animals requires the DNA glycosylase TDG or MBD4, which functions after oxidation or deamination of 5-methylcytosine, respectively. However, little is known about the steps following DNA glycosylase action in the active DNA demethylation pathways in plants and animals. We show here that the Arabidopsis APE1L protein has apurinic/apyrimidinic endonuclease activities and functions downstream of ROS1 and DME. APE1L and ROS1 interact in vitro and co-localize in vivo. Whole genome bisulfite sequencing of ape1l mutant plants revealed widespread alterations in DNA methylation. We show that the ape1l/zdp double mutant displays embryonic lethality. Notably, the ape1l+/-zdp-/- mutant shows a maternal-effect lethality phenotype. APE1L and the DNA phosphatase ZDP are required for FWA and MEA gene imprinting in the endosperm and are important for seed development. Thus, APE1L is a new component of the active DNA demethylation pathway and, together with ZDP, regulates gene imprinting in Arabidopsis.
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Affiliation(s)
- Yan Li
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Science, Peking University, Beijing, China
| | - Dolores Córdoba-Cañero
- Department of Genetics, University of Córdoba/Maimonides Institute for Biomedical Research of Cordoba (IMIBIC)/Reina Sofía University Hospital, Córdoba, Spain
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Science, Peking University, Beijing, China
| | - Xiaohong Zhu
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Kai Tang
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rafael R. Ariza
- Department of Genetics, University of Córdoba/Maimonides Institute for Biomedical Research of Cordoba (IMIBIC)/Reina Sofía University Hospital, Córdoba, Spain
| | - Teresa Roldán-Arjona
- Department of Genetics, University of Córdoba/Maimonides Institute for Biomedical Research of Cordoba (IMIBIC)/Reina Sofía University Hospital, Córdoba, Spain
- * E-mail: (TRA); (JKZ)
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail: (TRA); (JKZ)
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12
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Russell SD, Jones DS. The male germline of angiosperms: repertoire of an inconspicuous but important cell lineage. FRONTIERS IN PLANT SCIENCE 2015; 6:173. [PMID: 25852722 PMCID: PMC4367165 DOI: 10.3389/fpls.2015.00173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/03/2015] [Indexed: 05/03/2023]
Abstract
The male germline of flowering plants constitutes a specialized lineage of diminutive cells initiated by an asymmetric division of the initial microspore cell that sequesters the generative cell from the pollen vegetative cell. The generative cell subsequently divides to form the two male gametes (non-motile sperm cells) that fuse with the two female gametophyte target cells (egg and central cells) to form the zygote and endosperm. Although these male gametes can be as little as 1/800th of the volume of their female counterpart, they encode a highly distinctive and rich transcriptome, translate proteins, and display a novel suite of gamete-distinctive control elements that create a unique chromatin environment in the male lineage. Sperm-expressed transcripts also include a high proportion of transposable element-related sequences that may be targets of non-coding RNA including miRNA and silencing elements from peripheral cells. The number of sperm-encoded transcripts is somewhat fewer than the number present in the egg cell, but are remarkably distinct compared to other cell types according to principal component and other analyses. The molecular role of the male germ lineage cells is just beginning to be understood and appears more complex than originally anticipated.
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Affiliation(s)
- Scott D. Russell
- *Correspondence: Scott D. Russell, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, 770 Van Vleet Oval, OK 73019, USA
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13
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Wu DD, Wang X, Li Y, Zeng L, Irwin DM, Zhang YP. "Out of pollen" hypothesis for origin of new genes in flowering plants: study from Arabidopsis thaliana. Genome Biol Evol 2014; 6:2822-9. [PMID: 25237051 PMCID: PMC4224333 DOI: 10.1093/gbe/evu206] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
New genes, which provide material for evolutionary innovation, have been extensively studied for many years in animals where it is observed that they commonly show an expression bias for the testis. Thus, the testis is a major source for the generation of new genes in animals. The source tissue for new genes in plants is unclear. Here, we find that new genes in plants show a bias in expression to mature pollen, and are also enriched in a gene coexpression module that correlates with mature pollen in Arabidopsis thaliana. Transposable elements are significantly enriched in the new genes, and the high activity of transposable elements in the vegetative nucleus, compared with the germ cells, suggests that new genes are most easily generated in the vegetative nucleus in the mature pollen. We propose an "out of pollen" hypothesis for the origin of new genes in flowering plants.
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Affiliation(s)
- Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xin Wang
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
| | - Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - David M Irwin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada Banting and Best Diabetes Centre, University of Toronto, Toronto, Canada
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
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14
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El-Tantawy AA, Solís MT, Risueño MC, Testillano PS. Changes in DNA methylation levels and nuclear distribution patterns after microspore reprogramming to embryogenesis in barley. Cytogenet Genome Res 2014; 143:200-8. [PMID: 25074410 DOI: 10.1159/000365232] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Under specific stress treatments, the microspore can be induced in vitro to deviate from its gametophytic development and to reprogram towards embryogenesis, becoming a totipotent cell and forming haploid embryos. These can further regenerate homozygous plants for production of new isogenic lines, an important biotechnological tool for crop breeding. DNA methylation constitutes a prominent epigenetic modification of the chromatin fiber which regulates gene expression. Changes in DNA methylation accompany the reorganization of the nuclear architecture during plant cell differentiation and proliferation; however, the relationship between global DNA methylation and genome-wide expression patterns is still poorly understood. In this work, the dynamics of global DNA methylation levels and distribution patterns were analyzed during microspore reprogramming to embryogenesis and during pollen development in Hordeum vulgare. Quantification of global DNA methylation levels and 5-methyl-deoxycytidine (5mdC) immunofluorescence were conducted at specific stages of pollen development and after reprogramming to embryogenesis to analyze the epigenetic changes that accompany the change of developmental program and cell fate. The results showed low DNA methylation levels in microspores and a high increase along pollen development and maturation; an intense 5mdC signal was concentrated in the generative and sperm nuclei whereas the vegetative nucleus exhibited a weaker DNA methylation signal. After inductive stress treatment, low methylation levels and faint 5mdC signals were observed in nuclei of reprogrammed microspores and 2-4-cell proembryos. This data revealed a global DNA hypomethylation during the change of the developmental program and first embryogenic divisions. This is in contrast with the hypermethylation of generative and sperm cells of the male germline during pollen maturation, suggesting an epigenetic regulation after induction of microspore embryogenesis. At later embryogenesis stages, global DNA methylation progressively increased, accompanying embryo development and differentiation events like in zygotic embryos, corroborating that DNA methylation is critical for the regulation of gene expression in microspore embryogenesis.
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Affiliation(s)
- Ahmed-Abdalla El-Tantawy
- Pollen Biotechnology of Crop Plants Group, Centro de Investigaciones Biológicas, (CIB) CSIC, Madrid, Spain
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15
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Eichten SR, Schmitz RJ, Springer NM. Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation. PLANT PHYSIOLOGY 2014; 165:933-947. [PMID: 24872382 PMCID: PMC4081347 DOI: 10.1104/pp.113.234211] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Chromatin modifications and epigenetics may play important roles in many plant processes, including developmental regulation, responses to environmental stimuli, and local adaptation. Chromatin modifications describe biochemical changes to chromatin state, such as alterations in the specific type or placement of histones, modifications of DNA or histones, or changes in the specific proteins or RNAs that associate with a genomic region. The term epigenetic is often used to describe a variety of unexpected patterns of gene regulation or inheritance. Here, we specifically define epigenetics to include the key aspects of heritability (stable transmission of gene expression states through mitotic or meiotic cell divisions) and independence from DNA sequence changes. We argue against generically equating chromatin and epigenetics; although many examples of epigenetics involve chromatin changes, those chromatin changes are not always heritable or may be influenced by genetic changes. Careful use of the terms chromatin modifications and epigenetics can help separate the biochemical mechanisms of regulation from the inheritance patterns of altered chromatin states. Here, we also highlight examples in which chromatin modifications and epigenetics affect important plant processes.
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Affiliation(s)
- Steven R Eichten
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (S.R.E., N.M.S.); andDepartment of Genetics, University of Georgia, Athens, Georgia 30602 (R.J.S.)
| | - Robert J Schmitz
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (S.R.E., N.M.S.); andDepartment of Genetics, University of Georgia, Athens, Georgia 30602 (R.J.S.)
| | - Nathan M Springer
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (S.R.E., N.M.S.); andDepartment of Genetics, University of Georgia, Athens, Georgia 30602 (R.J.S.)
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16
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She W, Grimanelli D, Baroux C. An efficient method for quantitative, single-cell analysis of chromatin modification and nuclear architecture in whole-mount ovules in Arabidopsis. J Vis Exp 2014:e51530. [PMID: 24998753 PMCID: PMC4195603 DOI: 10.3791/51530] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In flowering plants, the somatic-to-reproductive cell fate transition is marked by the specification of spore mother cells (SMCs) in floral organs of the adult plant. The female SMC (megaspore mother cell, MMC) differentiates in the ovule primordium and undergoes meiosis. The selected haploid megaspore then undergoes mitosis to form the multicellular female gametophyte, which will give rise to the gametes, the egg cell and central cell, together with accessory cells. The limited accessibility of the MMC, meiocyte and female gametophyte inside the ovule is technically challenging for cytological and cytogenetic analyses at single cell level. Particularly, direct or indirect immunodetection of cellular or nuclear epitopes is impaired by poor penetration of the reagents inside the plant cell and single-cell imaging is demised by the lack of optical clarity in whole-mount tissues. Thus, we developed an efficient method to analyze the nuclear organization and chromatin modification at high resolution of single cell in whole-mount embedded Arabidopsis ovules. It is based on dissection and embedding of fixed ovules in a thin layer of acrylamide gel on a microscopic slide. The embedded ovules are subjected to chemical and enzymatic treatments aiming at improving tissue clarity and permeability to the immunostaining reagents. Those treatments preserve cellular and chromatin organization, DNA and protein epitopes. The samples can be used for different downstream cytological analyses, including chromatin immunostaining, fluorescence in situ hybridization (FISH), and DNA staining for heterochromatin analysis. Confocal laser scanning microscopy (CLSM) imaging, with high resolution, followed by 3D reconstruction allows for quantitative measurements at single-cell resolution.
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Affiliation(s)
- Wenjing She
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich
| | - Daniel Grimanelli
- Institut de Recherche pour le Développement (UMR 232), Centre National de la Recherche Scientifique (ERL 5300), Université de Montpellier II
| | - Célia Baroux
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich;
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17
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Anderson SN, Johnson CS, Jones DS, Conrad LJ, Gou X, Russell SD, Sundaresan V. Transcriptomes of isolated Oryza sativa gametes characterized by deep sequencing: evidence for distinct sex-dependent chromatin and epigenetic states before fertilization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:729-41. [PMID: 24215296 DOI: 10.1111/tpj.12336] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/12/2013] [Accepted: 09/19/2013] [Indexed: 05/19/2023]
Abstract
The formation of a zygote by the fusion of egg and sperm involves the two gametic transcriptomes. In flowering plants, the embryo sac embedded within the ovule contains the egg cell, whereas the pollen grain contains two sperm cells inside a supporting vegetative cell. The difficulties of collecting isolated gametes and consequent low recovery of RNA have restricted in-depth analysis of gametic transcriptomes in flowering plants. We isolated living egg cells, sperm cells and pollen vegetative cells from Oryza sativa (rice), and identified transcripts for approximately 36 000 genes by deep sequencing. The three transcriptomes are highly divergent, with about three-quarters of those genes differentially expressed in the different cell types. Distinctive expression profiles were observed for genes involved in chromatin conformation, including an unexpected expression in the sperm cell of genes associated with active chromatin. Furthermore, both the sperm cell and the pollen vegetative cell were deficient in expression of key RNAi components. Differences in gene expression were also observed for genes for hormonal signaling and cell cycle regulation. The egg cell and sperm cell transcriptomes reveal major differences in gene expression to be resolved in the zygote, including pathways affecting chromatin configuration, hormones and cell cycle. The sex-specific differences in the expression of RNAi components suggest that epigenetic silencing in the zygote might act predominantly through female-dependent pathways. More generally, this study provides a detailed gene expression landscape for flowering plant gametes, enabling the identification of specific gametic functions, and their contributions to zygote and seed development.
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Affiliation(s)
- Sarah N Anderson
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
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