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Bergis-Ser C, Reji M, Latrasse D, Bergounioux C, Benhamed M, Raynaud C. Chromatin dynamics and RNA metabolism are double-edged swords for the maintenance of plant genome integrity. NATURE PLANTS 2024; 10:857-873. [PMID: 38658791 DOI: 10.1038/s41477-024-01678-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
Maintenance of genome integrity is an essential process in all organisms. Mechanisms avoiding the formation of DNA lesions or mutations are well described in animals because of their relevance to human health and cancer. In plants, they are of growing interest because DNA damage accumulation is increasingly recognized as one of the consequences of stress. Although the cellular response to DNA damage is mostly studied in response to genotoxic treatments, the main source of DNA lesions is cellular activity itself. This can occur through the production of reactive oxygen species as well as DNA processing mechanisms such as DNA replication or transcription and chromatin dynamics. In addition, how lesions are formed and repaired is greatly influenced by chromatin features and dynamics and by DNA and RNA metabolism. Notably, actively transcribed regions or replicating DNA, because they are less condensed and are sites of DNA processing, are more exposed to DNA damage. However, at the same time, a wealth of cellular mechanisms cooperate to favour DNA repair at these genomic loci. These intricate relationships that shape the distribution of mutations along the genome have been studied extensively in animals but much less in plants. In this Review, we summarize how chromatin dynamics influence lesion formation and DNA repair in plants, providing a comprehensive view of current knowledge and highlighting open questions with regard to what is known in other organisms.
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Affiliation(s)
- Clara Bergis-Ser
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Meega Reji
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
- Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, India
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
- Université Paris Cité, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
- Institut Universitaire de France, Orsay, France
| | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France.
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2
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Mohanta TK, Mohanta YK, Kaushik P, Kumar J. Physiology, genomics, and evolutionary aspects of desert plants. J Adv Res 2024; 58:63-78. [PMID: 37160225 PMCID: PMC10982872 DOI: 10.1016/j.jare.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Despite the exposure to arid environmental conditions across the globe ultimately hampering the sustainability of the living organism, few plant species are equipped with several unique genotypic, biochemical, and physiological features to counter such harsh conditions. Physiologically, they have evolved with reduced leaf size, spines, waxy cuticles, thick leaves, succulent hydrenchyma, sclerophyll, chloroembryo, and photosynthesis in nonfoliar and other parts. At the biochemical level, they are evolved to perform efficient photosynthesis through Crassulacean acid metabolism (CAM) and C4 pathways with the formation of oxaloacetic acid (Hatch-Slack pathway) instead of the C3 pathway. Additionally, comparative genomics with existing data provides ample evidence of the xerophytic plants' positive selection to adapt to the arid environment. However, adding more high-throughput sequencing of xerophyte plant species is further required for a comparative genomic study toward trait discovery related to survival. Learning from the mechanism to survive in harsh conditions could pave the way to engineer crops for future sustainable agriculture. AIM OF THE REVIEW The distinct physiology of desert plants allows them to survive in harsh environments. However, the genomic composition also contributes significantly to this and requires great attention. This review emphasizes the physiological and genomic adaptation of desert plants. Other important parameters, such as desert biodiversity and photosynthetic strategy, are also discussed with recent progress in the field. Overall, this review discusses the different features of desert plants, which prepares them for harsh conditions intending to translate knowledge to engineer plant species for sustainable agriculture. KEY SCIENTIFIC CONCEPTS OF REVIEW This review comprehensively presents the physiology, molecular mechanism, and genomics of desert plants aimed towards engineering a sustainable crop.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 611, Oman.
| | - Yugal Kishore Mohanta
- Dept. of Applied Biology, University of Science and Technology Meghalaya, Baridua, Meghalaya 793101, India
| | - Prashant Kaushik
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Jitesh Kumar
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, United States
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3
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Szurman-Zubrzycka M, Jędrzejek P, Szarejko I. How Do Plants Cope with DNA Damage? A Concise Review on the DDR Pathway in Plants. Int J Mol Sci 2023; 24:ijms24032404. [PMID: 36768727 PMCID: PMC9916837 DOI: 10.3390/ijms24032404] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
DNA damage is induced by many factors, some of which naturally occur in the environment. Because of their sessile nature, plants are especially exposed to unfavorable conditions causing DNA damage. In response to this damage, the DDR (DNA damage response) pathway is activated. This pathway is highly conserved between eukaryotes; however, there are some plant-specific DDR elements, such as SOG1-a transcription factor that is a central DDR regulator in plants. In general, DDR signaling activates transcriptional and epigenetic regulators that orchestrate the cell cycle arrest and DNA repair mechanisms upon DNA damage. The cell cycle halts to give the cell time to repair damaged DNA before replication. If the repair is successful, the cell cycle is reactivated. However, if the DNA repair mechanisms fail and DNA lesions accumulate, the cell enters the apoptotic pathway. Thereby the proper maintenance of DDR is crucial for plants to survive. It is particularly important for agronomically important species because exposure to environmental stresses causing DNA damage leads to growth inhibition and yield reduction. Thereby, gaining knowledge regarding the DDR pathway in crops may have a huge agronomic impact-it may be useful in breeding new cultivars more tolerant to such stresses. In this review, we characterize different genotoxic agents and their mode of action, describe DDR activation and signaling and summarize DNA repair mechanisms in plants.
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4
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Brinkmeier J, Coelho S, de Massy B, Bourbon HM. Evolution and Diversity of the TopoVI and TopoVI-like Subunits With Extensive Divergence of the TOPOVIBL subunit. Mol Biol Evol 2022; 39:msac227. [PMID: 36256608 PMCID: PMC9665070 DOI: 10.1093/molbev/msac227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Type II DNA topoisomerases regulate topology by double-stranded DNA cleavage and ligation. The TopoVI family of DNA topoisomerase, first identified and biochemically characterized in Archaea, represents, with TopoVIII and mini-A, the type IIB family. TopoVI has several intriguing features in terms of function and evolution. TopoVI has been identified in some eukaryotes, and a global view is lacking to understand its evolutionary pattern. In addition, in eukaryotes, the two TopoVI subunits (TopoVIA and TopoVIB) have been duplicated and have evolved to give rise to Spo11 and TopoVIBL, forming TopoVI-like (TopoVIL), a complex essential for generating DNA breaks that initiate homologous recombination during meiosis. TopoVIL is essential for sexual reproduction. How the TopoVI subunits have evolved to ensure this meiotic function is unclear. Here, we investigated the phylogenetic conservation of TopoVI and TopoVIL. We demonstrate that BIN4 and RHL1, potentially interacting with TopoVIB, have co-evolved with TopoVI. Based on model structures, this observation supports the hypothesis for a role of TopoVI in decatenation of replicated chromatids and predicts that in eukaryotes the TopoVI catalytic complex includes BIN4 and RHL1. For TopoVIL, the phylogenetic analysis of Spo11, which is highly conserved among Eukarya, highlighted a eukaryal-specific N-terminal domain that may be important for its regulation. Conversely, TopoVIBL was poorly conserved, giving rise to ATP hydrolysis-mutated or -truncated protein variants, or was undetected in some species. This remarkable plasticity of TopoVIBL provides important information for the activity and function of TopoVIL during meiosis.
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Affiliation(s)
- Julia Brinkmeier
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier 34396, France
| | - Susana Coelho
- Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier 34396, France
| | - Henri-Marc Bourbon
- Centre de Biologie Intégrative, CNRS, Université de Toulouse, Toulouse 31400, France
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5
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Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading. Proc Natl Acad Sci U S A 2022; 119:e2001290119. [PMID: 35759655 PMCID: PMC9271158 DOI: 10.1073/pnas.2001290119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The organization of the genome into transcriptionally active and inactive chromatin domains requires well-delineated chromatin boundaries and insulator functions in order to maintain the identity of adjacent genomic loci with antagonistic chromatin marks and functionality. In plants that lack known chromatin insulators, the mechanisms that prevent heterochromatin spreading into euchromatin remain to be identified. Here, we show that DNA Topoisomerase VI participates in a chromatin boundary function that safeguards the expression of genes in euchromatin islands within silenced heterochromatin regions. While some transposable elements are reactivated in mutants of the Topoisomerase VI complex, genes insulated in euchromatin islands within heterochromatic regions of the Arabidopsis thaliana genome are specifically down-regulated. H3K9me2 levels consistently increase at euchromatin island loci and decrease at some transposable element loci. We further show that Topoisomerase VI physically interacts with S-adenosylmethionine synthase methionine adenosyl transferase 3 (MAT3), which is required for H3K9me2. A Topoisomerase VI defect affects MAT3 occupancy on heterochromatic elements and its exclusion from euchromatic islands, thereby providing a possible mechanistic explanation to the essential role of Topoisomerase VI in the delimitation of chromatin domains.
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6
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Inada N, Takahashi N, Umeda M. Arabidopsis thaliana subclass I ACTIN DEPOLYMERIZING FACTORs and vegetative ACTIN2/8 are novel regulators of endoreplication. JOURNAL OF PLANT RESEARCH 2021; 134:1291-1300. [PMID: 34282484 DOI: 10.1007/s10265-021-01333-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Endoreplication is a type of cell cycle where genome replication occurs without mitosis. An increase of ploidy level by endoreplication is often associated with cell enlargement and an enhanced plant growth. Here we report Arabidopsis thaliana subclass I ACTIN DEPOLYMERIZING FACTORs (ADFs) and vegetative ACTIN2/8 as novel regulators of endoreplication. A. thaliana has 11 ADF members that are divided into 4 subclasses. Subclass I consists of four members, ADF1, -2, -3, and -4, all of which constitutively express in various tissues. We found that both adf4 knockout mutant and transgenic plants in which expressions of all of four subclass I ADFs are suppressed (ADF1-4Ri) showed an increased leaf area of mature first leaves, which was associated with a significant increase of epidermal pavement cell area. Ploidy analysis revealed that the ploidy level was significantly increased in mature leaves of ADF1-4Ri. The increased ploidy was also observed in roots of adf4 and ADF1-4Ri, as well as in dark-grown hypocotyls of adf4. Furthermore, double mutants of vegetative ACT2 and ACT8 (act2/8) exhibited an increase of leaf area and ploidy level in mature leaves. Therefore, actin-relating pathway could regulate endoreplication. The possible mechanisms that actin and ADFs regulate endoreplication are discussed.
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Affiliation(s)
- Noriko Inada
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan.
| | - Naoki Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
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7
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McKie SJ, Neuman KC, Maxwell A. DNA topoisomerases: Advances in understanding of cellular roles and multi-protein complexes via structure-function analysis. Bioessays 2021; 43:e2000286. [PMID: 33480441 PMCID: PMC7614492 DOI: 10.1002/bies.202000286] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022]
Abstract
DNA topoisomerases, capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. As we review here, current structural approaches have revealed unprecedented insights into the complex DNA-topoisomerase interaction and strand passage mechanism, helping to advance our understanding of their activities in vivo. This has been complemented by single-molecule techniques, which have facilitated the detailed dissection of the various topoisomerase reactions. Recent work has also revealed the importance of topoisomerase interactions with accessory proteins and other DNA-associated proteins, supporting the idea that they often function as part of multi-enzyme assemblies in vivo. In addition, novel topoisomerases have been identified and explored, such as topo VIII and Mini-A. These new findings are advancing our understanding of DNA-related processes and the vital functions topos fulfil, demonstrating their indispensability in virtually every aspect of DNA metabolism.
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Affiliation(s)
- Shannon J. McKie
- Department Biological Chemistry, John Innes Centre, Norwich, UK
- Laboratory of Single Molecule Biophysics, NHLBI, Bethesda, Maryland, USA
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, Bethesda, Maryland, USA
| | - Anthony Maxwell
- Department Biological Chemistry, John Innes Centre, Norwich, UK
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8
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Oliver J, Fan M, McKinley B, Zemelis‐Durfee S, Brandizzi F, Wilkerson C, Mullet JE. The AGCVIII kinase Dw2 modulates cell proliferation, endomembrane trafficking, and MLG/xylan cell wall localization in elongating stem internodes of Sorghum bicolor. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1053-1071. [PMID: 33211340 PMCID: PMC7983884 DOI: 10.1111/tpj.15086] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 05/31/2023]
Abstract
Stems of bioenergy sorghum (Sorghum bicolor L. Moench.), a drought-tolerant C4 grass, contain up to 50 nodes and internodes of varying length that span 4-5 m and account for approximately 84% of harvested biomass. Stem internode growth impacts plant height and biomass accumulation and is regulated by brassinosteroid signaling, auxin transport, and gibberellin biosynthesis. In addition, an AGCVIII kinase (Dw2) regulates sorghum stem internode growth, but the underlying mechanism and signaling network are unknown. Here we provide evidence that mutation of Dw2 reduces cell proliferation in internode intercalary meristems, inhibits endocytosis, and alters the distribution of heteroxylan and mixed linkage glucan in cell walls. Phosphoproteomic analysis showed that Dw2 signaling influences the phosphorylation of proteins involved in lipid signaling (PLDδ), endomembrane trafficking, hormone, light, and receptor signaling, and photosynthesis. Together, our results show that Dw2 modulates endomembrane function and cell division during sorghum internode growth, providing insight into the regulation of monocot stem development.
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Affiliation(s)
- Joel Oliver
- Department of Biochemistry & BiophysicsTexas A&M UniversityCollege StationTexas77843USA
| | - Mingzhu Fan
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824USA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichigan48824USA
| | - Brian McKinley
- Department of Biochemistry & BiophysicsTexas A&M UniversityCollege StationTexas77843USA
| | - Starla Zemelis‐Durfee
- MSU‐DOE Plant Research LabMichigan State UniversityEast LansingMichigan48824USA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichigan48824USA
| | - Federica Brandizzi
- MSU‐DOE Plant Research LabMichigan State UniversityEast LansingMichigan48824USA
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824USA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichigan48824USA
| | - Curtis Wilkerson
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824USA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichigan48824USA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichigan48824USA
| | - John E. Mullet
- Department of Biochemistry & BiophysicsTexas A&M UniversityCollege StationTexas77843USA
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9
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Sutormin DA, Galivondzhyan AK, Polkhovskiy AV, Kamalyan SO, Severinov KV, Dubiley SA. Diversity and Functions of Type II Topoisomerases. Acta Naturae 2021; 13:59-75. [PMID: 33959387 PMCID: PMC8084294 DOI: 10.32607/actanaturae.11058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/09/2020] [Indexed: 11/29/2022] Open
Abstract
The DNA double helix provides a simple and elegant way to store and copy genetic information. However, the processes requiring the DNA helix strands separation, such as transcription and replication, induce a topological side-effect - supercoiling of the molecule. Topoisomerases comprise a specific group of enzymes that disentangle the topological challenges associated with DNA supercoiling. They relax DNA supercoils and resolve catenanes and knots. Here, we review the catalytic cycles, evolution, diversity, and functional roles of type II topoisomerases in organisms from all domains of life, as well as viruses and other mobile genetic elements.
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Affiliation(s)
- D. A. Sutormin
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - A. K. Galivondzhyan
- Lomonosov Moscow State University, Moscow, 119991 Russia
- Institute of Molecular Genetics RAS, Moscow, 123182 Russia
| | - A. V. Polkhovskiy
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - S. O. Kamalyan
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - K. V. Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Centre for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
- Waksman Institute for Microbiology, Piscataway, New Jersey, 08854 USA
| | - S. A. Dubiley
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
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10
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Bhosale R, Maere S, De Veylder L. Endoreplication as a potential driver of cell wall modifications. CURRENT OPINION IN PLANT BIOLOGY 2019; 51:58-65. [PMID: 31071565 DOI: 10.1016/j.pbi.2019.04.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 05/06/2023]
Abstract
Endoreplication represents a variant of the mitotic cell cycle during which cells replicate their DNA without mitosis and/or cytokinesis, resulting in an increase in the cells' ploidy level. This process is especially prominent in higher plants, where it has been correlated with cell differentiation, metabolic output and rapid cell growth. However, different reports argue against a ploidy-dependent contribution to cell growth. Here, we review accumulating data suggesting that endocycle onset might exert an effect on cell growth through transcriptional control of cell wall-modifying genes to drive cell wall changes required to accommodate turgor-driven rapid cell expansion, consistent with the idea that vacuolar expansion rather than a ploidy-driven increase in cellular volume represents the major force driving cell growth.
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Affiliation(s)
- Rahul Bhosale
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, United Kingdom; Center for Plant Integrative Biology (CPIB), University of Nottingham, Sutton Bonington, LE12 5RD, United Kingdom
| | - Steven Maere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium.
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11
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Wei Z, Shi X, Wei F, Fan Z, Mei L, Tian B, Shi Y, Cao G, Shi G. The cotton endocycle-involved protein SPO11-3 functions in salt stress via integrating leaf stomatal response, ROS scavenging and root growth. PHYSIOLOGIA PLANTARUM 2019; 167:127-141. [PMID: 30426499 DOI: 10.1111/ppl.12875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 11/04/2018] [Accepted: 11/08/2018] [Indexed: 06/09/2023]
Abstract
The SPORULATION 11 (SPO11) proteins are among eukaryotic the topoisomerase VIA (Topo VIA) homologs involved in modulating various important biological processes, such as growth, development and stress response via endoreduplication in plants, but the underlying mechanism response to stress remains largely unknown under salt treatment. Here, we attempted to characterize a homolog of TOP VIA in upland cotton (Gossypium hirsutum L.), designated as GhSPO11-3. The silencing of GhSPO11-3 in cotton plants resulted in a dwarf phenotype with a failure of cell endoreduplication and a phase shift in the ploidy levels. The GhSPO11-3-silenced plants also showed substantial changes including accumulated malondialdehyde, significantly reduced chlorophyll and proline contents and decreased antioxidative enzyme activity after salt treatment. In addition, transgenic Arabidopsis lines overexpressing GhSPO11-3 accelerated both leaf and root growth with cell expansion and endopolyploidy. Both leaf stomatal density and aperture were markedly decreased, and the transgenic Arabidopsis lines were more tolerant with expression of stress-responsive genes under salinity stress. Furthermore, consistent with the reduced reactive oxygen species (ROS), the expression of ROS scavenging-related genes was largely reinforced, and antioxidant enzyme activities were accordingly significantly enhanced in transgenic Arabidopsis lines under salt stress. In general, these results indicated that GhSPO11-3 likely respond to salt stress by positively regulating root growth, stomatal response, ROS production and the expression of stress-related genes to cope with adverse conditions in plants.
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Affiliation(s)
- Zhenzhen Wei
- Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, Henan 450001, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xinjie Shi
- Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, Henan 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Fang Wei
- Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, Henan 450001, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Zhuxuan Fan
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Liqing Mei
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Baoming Tian
- Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, Henan 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yinghui Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Gangqiang Cao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Gongyao Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
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12
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Kim JH, Ryu TH, Lee SS, Lee S, Chung BY. Ionizing radiation manifesting DNA damage response in plants: An overview of DNA damage signaling and repair mechanisms in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 278:44-53. [PMID: 30471728 DOI: 10.1016/j.plantsci.2018.10.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/30/2018] [Accepted: 10/16/2018] [Indexed: 05/23/2023]
Abstract
Plants orchestrate various DNA damage responses (DDRs) to overcome the deleterious impacts of genotoxic agents on genetic materials. Ionizing radiation (IR) is widely used as a potent genotoxic agent in plant DDR research as well as plant breeding and quarantine services for commercial uses. This review aimed to highlight the recent advances in cellular and phenotypic DDRs, especially those induced by IR. Various physicochemical genotoxic agents damage DNA directly or indirectly by inhibiting DNA replication. Among them, IR-induced DDRs are considerably more complicated. Many aspects of such DDRs and their initial transcriptomes are closely related to oxidative stress response. Although many key components of DDR signaling have been characterized in plants, DDRs in plant cells are not understood in detail to allow comparison with those in yeast and mammalian cells. Recent studies have revealed plant DDR signaling pathways including the key regulator SOG1. The SOG1 and its upstream key components ATM and ATR could be functionally characterized by analyzing their knockout DDR phenotypes after exposure to IR. Considering the potent genotoxicity of IR and its various DDR phenotypes, IR-induced DDR studies should help to establish an integrated model for plant DDR signaling pathways by revealing the unknown key components of various DDRs in plants.
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Affiliation(s)
- Jin-Hong Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea; Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
| | - Tae Ho Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Seung Sik Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea; Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Sungbeom Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea; Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Byung Yeoup Chung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
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13
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Bhosale R, Boudolf V, Cuevas F, Lu R, Eekhout T, Hu Z, Van Isterdael G, Lambert GM, Xu F, Nowack MK, Smith RS, Vercauteren I, De Rycke R, Storme V, Beeckman T, Larkin JC, Kremer A, Höfte H, Galbraith DW, Kumpf RP, Maere S, De Veylder L. A Spatiotemporal DNA Endoploidy Map of the Arabidopsis Root Reveals Roles for the Endocycle in Root Development and Stress Adaptation. THE PLANT CELL 2018; 30:2330-2351. [PMID: 30115738 PMCID: PMC6241279 DOI: 10.1105/tpc.17.00983] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 06/18/2018] [Accepted: 08/08/2018] [Indexed: 05/21/2023]
Abstract
Somatic polyploidy caused by endoreplication is observed in arthropods, molluscs, and vertebrates but is especially prominent in higher plants, where it has been postulated to be essential for cell growth and fate maintenance. However, a comprehensive understanding of the physiological significance of plant endopolyploidy has remained elusive. Here, we modeled and experimentally verified a high-resolution DNA endoploidy map of the developing Arabidopsis thaliana root, revealing a remarkable spatiotemporal control of DNA endoploidy levels across tissues. Fitting of a simplified model to publicly available data sets profiling root gene expression under various environmental stress conditions suggested that this root endoploidy patterning may be stress-responsive. Furthermore, cellular and transcriptomic analyses revealed that inhibition of endoreplication onset alters the nuclear-to-cellular volume ratio and the expression of cell wall-modifying genes, in correlation with the appearance of cell structural changes. Our data indicate that endopolyploidy might serve to coordinate cell expansion with structural stability and that spatiotemporal endoreplication pattern changes may buffer for stress conditions, which may explain the widespread occurrence of the endocycle in plant species growing in extreme or variable environments.
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Affiliation(s)
- Rahul Bhosale
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Veronique Boudolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Fabiola Cuevas
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Ran Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Zhubing Hu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 475004 Kaifeng, China
| | - Gert Van Isterdael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
- VIB Flow Core, B-9052 Ghent, Belgium
| | | | - Fan Xu
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Riet De Rycke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
- VIB Bio Imaging Core, B-9052 Ghent, Belgium
| | - Veronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - John C Larkin
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Anna Kremer
- Center for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
- VIB Bio Imaging Core, B-9052 Ghent, Belgium
| | - Herman Höfte
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - David W Galbraith
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Robert P Kumpf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Steven Maere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
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14
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Wendorff TJ, Berger JM. Topoisomerase VI senses and exploits both DNA crossings and bends to facilitate strand passage. eLife 2018; 7:31724. [PMID: 29595473 PMCID: PMC5922973 DOI: 10.7554/elife.31724] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 03/28/2018] [Indexed: 01/09/2023] Open
Abstract
Type II topoisomerases manage DNA supercoiling and aid chromosome segregation using a complex, ATP-dependent duplex strand passage mechanism. Type IIB topoisomerases and their homologs support both archaeal/plant viability and meiotic recombination. Topo VI, a prototypical type IIB topoisomerase, comprises two Top6A and two Top6B protomers; how these subunits cooperate to engage two DNA segments and link ATP turnover to DNA transport is poorly understood. Using multiple biochemical approaches, we show that Top6B, which harbors the ATPase activity of topo VI, recognizes and exploits the DNA crossings present in supercoiled DNA to stimulate subunit dimerization by ATP. Top6B self-association in turn induces extensive DNA bending, which is needed to support duplex cleavage by Top6A. Our observations explain how topo VI tightly coordinates DNA crossover recognition and ATP binding with strand scission, providing useful insights into the operation of type IIB topoisomerases and related meiotic recombination and GHKL ATPase machineries. Each human cell contains genetic information stored on approximately two meters of DNA. Like holiday lights in a storage box, packing so much DNA into such a small space leads to its entanglement. This snarled DNA prevents the cell from properly accessing and copying its genes. Type II topoisomerases are a group of enzymes that remove DNA tangles. They attach to one segment of a DNA tangle, cut it in half, remove the knot, and then repair the broken DNA strand. The process requires the proteins to ‘burn’ chemical energy. If topoisomerases make mistakes when they cut and reseal DNA, they could damage genetic information and harm cells. It is still unclear how these proteins recognize DNA tangles and use energy to remove knots instead of adding them. Here, Wendorff and Berger use biochemical approaches to look into topo VI, a type II topoisomerase found in plants and certain single-celled organisms. When DNA is tangled, it forms sharp bends and crossings. Their experiments reveal that topo VI has certain ‘sensors’ that detect where DNA bends, and others that recognize the crossings. Only when both features are present does the enzyme start working and using energy. These sensors act as fail-safes to ensure that topo VI only breaks DNA when it encounters a proper knot, and is not ‘set loose’ on untangled DNA. Future work will look at topo VI at an atom-by-atom level to reveal how exactly the enzymes ‘see’ DNA bends and crossings, and how interactions with the correct type of DNA triggers energy use and DNA untangling. Knowing more about topo VI can help researchers to understand how human and bacterial topoisomerases work. These results could also be generalized to other enzymes, for example those that help the genetic processes at play when sperm and egg cells form.
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Affiliation(s)
- Timothy J Wendorff
- Biophysics Graduate Program, University of California, Berkeley, Berkeley, United States
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
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15
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Shibata M, Breuer C, Kawamura A, Clark NM, Rymen B, Braidwood L, Morohashi K, Busch W, Benfey PN, Sozzani R, Sugimoto K. GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis. Development 2018; 145:145/3/dev159707. [PMID: 29439132 PMCID: PMC5818008 DOI: 10.1242/dev.159707] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 01/09/2018] [Indexed: 01/17/2023]
Abstract
How plants determine the final size of growing cells is an important, yet unresolved, issue. Root hairs provide an excellent model system with which to study this as their final cell size is remarkably constant under constant environmental conditions. Previous studies have demonstrated that a basic helix-loop helix transcription factor ROOT HAIR DEFECTIVE 6-LIKE 4 (RSL4) promotes root hair growth, but how hair growth is terminated is not known. In this study, we demonstrate that a trihelix transcription factor GT-2-LIKE1 (GTL1) and its homolog DF1 repress root hair growth in Arabidopsis. Our transcriptional data, combined with genome-wide chromatin-binding data, show that GTL1 and DF1 directly bind the RSL4 promoter and regulate its expression to repress root hair growth. Our data further show that GTL1 and RSL4 regulate each other, as well as a set of common downstream genes, many of which have previously been implicated in root hair growth. This study therefore uncovers a core regulatory module that fine-tunes the extent of root hair growth by the orchestrated actions of opposing transcription factors. Summary:Arabidopsis gtl1 df1 double mutants and tissue-specific overexpression of GTL1 and DF1 demonstrate that both GTL1 and DF1 negatively regulate root hair growth by directly repressing RSL4.
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Affiliation(s)
- Michitaro Shibata
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Christian Breuer
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Ayako Kawamura
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27708, USA.,Biomathematics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Bart Rymen
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Luke Braidwood
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Kengo Morohashi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda 278-8510, Japan
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Philip N Benfey
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC 27695, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27708, USA.,Biomathematics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
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16
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Wildermuth MC, Steinwand MA, McRae AG, Jaenisch J, Chandran D. Adapted Biotroph Manipulation of Plant Cell Ploidy. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:537-564. [PMID: 28617655 DOI: 10.1146/annurev-phyto-080516-035458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Diverse plant biotrophs that establish a sustained site of nutrient acquisition induce localized host endoreduplication. Endoreduplication is a process by which cells successively replicate their genomes without mitosis, resulting in an increase in nuclear DNA ploidy. Elevated ploidy is associated with enhanced cell size, metabolic capacity, and the capacity to differentiate. Localized host endoreduplication induced by adapted plant biotrophs promotes biotroph colonization, development, and/or proliferation. When induced host endoreduplication is limited, biotroph growth and/or development are compromised. Herein, we examine a diverse set of plant-biotroph interactions to identify (a) common host components manipulated to promote induced host endoreduplication and (b) biotroph effectors that facilitate this induced host process. Shared mechanisms to promote host endoreduplication and development of nutrient exchange/feeding sites include manipulation centered on endocycle entry at the G2-M transition as well as yet undefined roles for differentiation regulators (e.g., CLE peptides) and pectin/cell wall modification.
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Affiliation(s)
- Mary C Wildermuth
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720;
| | - Michael A Steinwand
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720;
| | - Amanda G McRae
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720;
| | - Johan Jaenisch
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720;
| | - Divya Chandran
- Regional Center for Biotechnology, NCR Biotech Science Cluster, Faridabad, India 121001
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17
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Ploidy-dependent changes in the epigenome of symbiotic cells correlate with specific patterns of gene expression. Proc Natl Acad Sci U S A 2017; 114:4543-4548. [PMID: 28404731 DOI: 10.1073/pnas.1704211114] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The formation of symbiotic nodule cells in Medicago truncatula is driven by successive endoreduplication cycles and transcriptional reprogramming in different temporal waves including the activation of more than 600 cysteine-rich NCR genes expressed only in nodules. We show here that the transcriptional waves correlate with growing ploidy levels and have investigated how the epigenome changes during endoreduplication cycles. Differential DNA methylation was found in only a small subset of symbiotic nodule-specific genes, including more than half of the NCR genes, whereas in most genes DNA methylation was unaffected by the ploidy levels and was independent of the genes' active or repressed state. On the other hand, expression of nodule-specific genes correlated with ploidy-dependent opening of the chromatin as well as, in a subset of tested genes, with reduced H3K27me3 levels combined with enhanced H3K9ac levels. Our results suggest that endoreduplication-dependent epigenetic changes contribute to transcriptional reprogramming in the differentiation of symbiotic cells.
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18
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Poulet A, Duc C, Voisin M, Desset S, Tutois S, Vanrobays E, Benoit M, Evans DE, Probst AV, Tatout C. The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants. J Cell Sci 2017; 130:590-601. [PMID: 28049722 DOI: 10.1242/jcs.194712] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/04/2016] [Indexed: 12/20/2022] Open
Abstract
The linker of nucleoskeleton and cytoskeleton (LINC) complex is an evolutionarily well-conserved protein bridge connecting the cytoplasmic and nuclear compartments across the nuclear membrane. While recent data support its function in nuclear morphology and meiosis, its involvement in chromatin organisation has not been studied in plants. Here, 3D imaging methods have been used to investigate nuclear morphology and chromatin organisation in interphase nuclei of the model plant Arabidopsis thaliana in which heterochromatin clusters in conspicuous chromatin domains called chromocentres. Chromocentres form a repressive chromatin environment contributing to transcriptional silencing of repeated sequences, a general mechanism needed for genome stability. Quantitative measurements of the 3D position of chromocentres indicate their close proximity to the nuclear periphery but that their position varies with nuclear volume and can be altered in specific mutants affecting the LINC complex. Finally, we propose that the plant LINC complex contributes to proper heterochromatin organisation and positioning at the nuclear periphery, since its alteration is associated with the release of transcriptional silencing as well as decompaction of heterochromatic sequences.
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Affiliation(s)
- Axel Poulet
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France.,Sainsbury Laboratory Cambridge, University of Cambridge, Cambridge CB2 1LR, UK
| | - Céline Duc
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Maxime Voisin
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Sophie Desset
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Sylvie Tutois
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Emmanuel Vanrobays
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Matthias Benoit
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - David E Evans
- Sainsbury Laboratory Cambridge, University of Cambridge, Cambridge CB2 1LR, UK
| | - Aline V Probst
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Christophe Tatout
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
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19
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Chandran D, Wildermuth M. Modulation of Host Endocycle During Plant–Biotroph Interactions. DEVELOPMENTAL SIGNALING IN PLANTS 2016; 40:65-103. [DOI: 10.1016/bs.enz.2016.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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Ikeuchi M, Iwase A, Sugimoto K. Control of plant cell differentiation by histone modification and DNA methylation. CURRENT OPINION IN PLANT BIOLOGY 2015; 28:60-7. [PMID: 26454697 DOI: 10.1016/j.pbi.2015.09.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/03/2015] [Accepted: 09/05/2015] [Indexed: 05/10/2023]
Abstract
How cells differentiate and acquire diverse arrays of determined states in multicellular organisms is a fundamental and yet unanswered question in biology. Molecular genetic studies over the last few decades have identified many transcriptional regulators that activate or repress gene expression to promote cell differentiation in plant development. What has recently emerged as an additional important regulatory layer is the control at the epigenetic level by which locus-specific DNA methylation and histone modification alter the chromatin state and limit the expression of key developmental regulators to specific windows of time and space. Accumulating evidence suggests that histone acetylation is commonly linked with active transcription and this mechanism is adopted to control sequential progression of cell differentiation. Histone H3 trimethylation at lysine 27 and DNA methylation are both associated with gene repression, and these mechanisms are often utilised to promote and/or maintain the differentiated status of plant cells.
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Affiliation(s)
- Momoko Ikeuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Iwase
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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21
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Ikeuchi M, Iwase A, Rymen B, Harashima H, Shibata M, Ohnuma M, Breuer C, Morao AK, de Lucas M, De Veylder L, Goodrich J, Brady SM, Roudier F, Sugimoto K. PRC2 represses dedifferentiation of mature somatic cells in Arabidopsis. NATURE PLANTS 2015; 1:15089. [PMID: 27250255 DOI: 10.1038/nplants.2015.89] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 05/29/2015] [Indexed: 05/18/2023]
Abstract
Plant somatic cells are generally acknowledged to retain totipotency, the potential to develop into any cell type within an organism. This astonishing plasticity may contribute to a high regenerative capacity on severe damage, but how plants control this potential during normal post-embryonic development remains largely unknown(1,2). Here we show that POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a chromatin regulator that maintains gene repression through histone modification, prevents dedifferentiation of mature somatic cells in Arabidopsis thaliana roots. Loss-of-function mutants in PRC2 subunits initially develop unicellular root hairs indistinguishable from those in wild type but fail to retain the differentiated state, ultimately resulting in the generation of an unorganized cell mass and somatic embryos from a single root hair. Strikingly, mutant root hairs complete the normal endoreduplication programme, increasing their nuclear ploidy, but subsequently reinitiate mitotic division coupled with successive DNA replication. Our data show that the WOUND INDUCED DEDIFFERENTIATION3 (WIND3) and LEAFY COTYLEDON2 (LEC2) genes are among the PRC2 targets involved in this reprogramming, as their ectopic overexpression partly phenocopies the dedifferentiation phenotype of PRC2 mutants. These findings unveil the pivotal role of PRC2-mediated gene repression in preventing unscheduled reprogramming of fully differentiated plant cells.
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Affiliation(s)
- Momoko Ikeuchi
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Iwase
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Bart Rymen
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hirofumi Harashima
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Michitaro Shibata
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mariko Ohnuma
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Christian Breuer
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Ana Karina Morao
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, Paris Cedex 05 75230, France
| | - Miguel de Lucas
- Department of Plant Biology and Genome Center, University of California, Davis, 1002 Life Sciences, One Shields Avenue, Davis, California 95616, USA
| | - Lieven De Veylder
- Department of Plant Systems Biology, VIB, Gent B-9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent B-9052, Belgium
| | - Justin Goodrich
- Institute of Molecular Plant Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, 1002 Life Sciences, One Shields Avenue, Davis, California 95616, USA
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, Paris Cedex 05 75230, France
| | - Keiko Sugimoto
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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22
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Robinson DO, Roeder AHK. Themes and variations in cell type patterning in the plant epidermis. Curr Opin Genet Dev 2015; 32:55-65. [PMID: 25727387 DOI: 10.1016/j.gde.2015.01.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/26/2015] [Accepted: 01/27/2015] [Indexed: 01/16/2023]
Abstract
It has recently become evident that plant development, like animal development, has molecular patterning modules that are reused again and again to create different cell type patterns. Here we focus on three of these plant modules: (1) the MYB-bHLH-WD40 protein complex, (2) the transmembrane calpain protease DEFECTIVE KERNEL1 (DEK1), and (3) homeodomain leucine zipper (HD-ZIP) class IV transcription factors acting in concert with SIAMESE-related cyclin-dependent kinase inhibitors. These three modules initiate the patterning of multiple cell types in the plant epidermis: the regular spacing of trichomes (leaf hairs), the stripes of root hairs, diverse pigmentation patterns in petals, the scattering of giant cells, and the files of bulliform cells. Varied combinations of players and additional regulatory inputs partially account for the diversity of patterns that are generated by reusing the same molecular mechanisms.
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Affiliation(s)
- Dana Olivia Robinson
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA.
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23
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Suzaki T, Yoro E, Kawaguchi M. Leguminous plants: inventors of root nodules to accommodate symbiotic bacteria. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 316:111-58. [PMID: 25805123 DOI: 10.1016/bs.ircmb.2015.01.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Legumes and a few other plant species can establish a symbiotic relationship with nitrogen-fixing rhizobia, which enables them to survive in a nitrogen-deficient environment. During the course of nodulation, infection with rhizobia induces the dedifferentiation of host cells to form primordia of a symbiotic organ, the nodule, which prepares plants to accommodate rhizobia in host cells. While these nodulation processes are known to be genetically controlled by both plants and rhizobia, recent advances in studies on two model legumes, Lotus japonicus and Medicago truncatula, have provided great insight into the underlying plant-side molecular mechanism. In this chapter, we review such knowledge, with particular emphasis on two key processes of nodulation, nodule development and rhizobial invasion.
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Affiliation(s)
- Takuya Suzaki
- National Institute for Basic Biology, Okazaki, Japan; School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan
| | - Emiko Yoro
- National Institute for Basic Biology, Okazaki, Japan; School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Okazaki, Japan; School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan
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Hisanaga T, Kawade K, Tsukaya H. Compensation: a key to clarifying the organ-level regulation of lateral organ size in plants. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1055-63. [PMID: 25635111 DOI: 10.1093/jxb/erv028] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Leaves are ideal model systems to study the organ size regulation of multicellular plants. Leaf cell number and cell size are determinant factors of leaf size which is controlled through cell proliferation and post-mitotic cell expansion, respectively. To achieve a proper leaf size, cell proliferation and post-mitotic cell expansion should be co-ordinated during leaf morphogenesis. Compensation, which is enhanced post-mitotic cell expansion associated with a decrease in cell number during lateral organ development, is suggestive of such co-ordination. Genetic and kinematic studies revealed at least three classes of modes of compensation, indicating that compensation is a heterogeneous phenomenon. Recent studies have increased our understanding about the molecular basis of compensation by identifying the causal genes of each compensation-exhibiting mutant. Furthermore, analyses using chimeric leaves revealed that a type of compensated cell expansion requires cell-to-cell communication. Information from recent advances in molecular and genetic studies on compensation has been integrated here and its role in organ size regulation is discussed.
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Affiliation(s)
- Tetsuya Hisanaga
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Kensuke Kawade
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Hirokazu Tsukaya
- Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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Mittal A, Balasubramanian R, Cao J, Singh P, Subramanian S, Hicks G, Nothnagel EA, Abidi N, Janda J, Galbraith DW, Rock CD. TOPOISOMERASE 6B is involved in chromatin remodelling associated with control of carbon partitioning into secondary metabolites and cell walls, and epidermal morphogenesis in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4217-39. [PMID: 24821950 PMCID: PMC4112631 DOI: 10.1093/jxb/eru198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plant growth is continuous and modular, a combination that allows morphogenesis by cell division and elongation and serves to facilitate adaptation to changing environments. The pleiotropic phenotypes of the harlequin (hlq) mutant, isolated on the basis of ectopic expression of the abscisic acid (ABA)- and auxin-inducible proDc3:GUS reporter gene, were previously characterized. Mutants are skotomorphogenic, have deformed and collapsed epidermal cells which accumulate callose and starch, cell walls abundant in pectins and cell wall proteins, and abnormal and reduced root hairs and leaf trichomes. hlq and two additional alleles that vary in their phenotypic severity of starch accumulation in the light and dark have been isolated, and it is shown that they are alleles of bin3/hyp6/rhl3/Topoisomerase6B. Mutants and inhibitors affecting the cell wall phenocopy several of the traits displayed in hlq. A microarray analysis was performed, and coordinated expression of physically adjacent pairs/sets of genes was observed in hlq, suggesting a direct effect on chromatin. Histones, WRKY and IAA/AUX transcription factors, aquaporins, and components of ubiquitin-E3-ligase-mediated proteolysis, and ABA or biotic stress response markers as well as proteins involved in cellular processes affecting carbon partitioning into secondary metabolites were also identified. A comparative analysis was performed of the hlq transcriptome with other previously published TopoVI mutant transcriptomes, namely bin3, bin5, and caa39 mutants, and limited concordance between data sets was found, suggesting indirect or genotype-specific effects. The results shed light on the molecular mechanisms underlying the det/cop/fus-like pleiotropic phenotypes of hlq and support a broader role for TopoVI regulation of chromatin remodelling to mediate development in response to environmental and hormonal signals.
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Affiliation(s)
- Amandeep Mittal
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Rajagopal Balasubramanian
- Tamil Nadu Agricultural University, Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Madurai-625 104, India
| | - Jin Cao
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143 005, Punjab, India
| | - Senthil Subramanian
- South Dakota State University, Department of Plant Science, Brookings, SD 57007, USA
| | - Glenn Hicks
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA Department of Botany and Plant Sciences, University of California, Riverside CA 92521-0124, USA
| | - Eugene A Nothnagel
- Department of Botany and Plant Sciences, University of California, Riverside CA 92521-0124, USA
| | - Noureddine Abidi
- Texas Tech University, Department of Plant and Soil Science and Fiber and Biopolymer Research Institute, 1001 East Loop 289, Lubbock, TX 79409-5019, USA
| | - Jaroslav Janda
- University of Arizona, Department of Plant Sciences and BIO5 Institute, 341 Keating Bldg, Tucson, AZ 85721, USA
| | - David W Galbraith
- University of Arizona, Department of Plant Sciences and BIO5 Institute, 341 Keating Bldg, Tucson, AZ 85721, USA
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
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Grierson C, Nielsen E, Ketelaarc T, Schiefelbein J. Root hairs. THE ARABIDOPSIS BOOK 2014; 12:e0172. [PMID: 24982600 PMCID: PMC4075452 DOI: 10.1199/tab.0172] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Roots hairs are cylindrical extensions of root epidermal cells that are important for acquisition of nutrients, microbe interactions, and plant anchorage. The molecular mechanisms involved in the specification, differentiation, and physiology of root hairs in Arabidopsis are reviewed here. Root hair specification in Arabidopsis is determined by position-dependent signaling and molecular feedback loops causing differential accumulation of a WD-bHLH-Myb transcriptional complex. The initiation of root hairs is dependent on the RHD6 bHLH gene family and auxin to define the site of outgrowth. Root hair elongation relies on polarized cell expansion at the growing tip, which involves multiple integrated processes including cell secretion, endomembrane trafficking, cytoskeletal organization, and cell wall modifications. The study of root hair biology in Arabidopsis has provided a model cell type for insights into many aspects of plant development and cell biology.
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Affiliation(s)
- Claire Grierson
- School of Biological Sciences, University of Bristol, Bristol, UK BS8 1UG
| | - Erik Nielsen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA 48109
| | - Tijs Ketelaarc
- Laboratory of Cell Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA 48109
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Morphological, genetic and molecular characteristics of barley root hair mutants. J Appl Genet 2014; 55:433-47. [PMID: 24899566 PMCID: PMC4185097 DOI: 10.1007/s13353-014-0225-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 11/21/2022]
Abstract
Root hairs are tubular outgrowths of specialized epidermal cells called trichoblasts. They affect anchoring plants in soil, the uptake of water and nutrients and are the sites of the interaction between plants and microorganisms. Nineteen root hair mutants of barley representing different stages of root hair development were subjected to detailed morphological and genetic analyses. Each mutant was monogenic and recessive. An allelism test revealed that nine loci were responsible for the mutated root hair phenotypes in the collection and 1–4 mutated allelic forms were identified at each locus. Genetic relationships between the genes responsible for different stages of root hair formation were established. The linkage groups of four loci rhl1, rhp1, rhi1 and rhs1, which had previously been mapped on chromosomes 7H, 1H, 6H and 5H, respectively, were enriched with new markers that flank the genes at a distance of 0.16 cM to 4.6 cM. The chromosomal position of three new genes – two that are responsible for the development of short root hairs (rhs2 and rhs3) and the gene that controls an irregular root hair pattern (rhi2) – were mapped on chromosomes 6H, 2H and 1H, respectively. A comparative analysis of the agrobotanical parameters between some mutants and their respective parental lines showed that mutations in genes responsible for root hair development had no effect on the agrobotanical performance of plants that were grown under controlled conditions. The presented mutant collection is a valuable tool for further identification of genes controlling root hair development in barley.
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Yoon HJ, Hossain MS, Held M, Hou H, Kehl M, Tromas A, Sato S, Tabata S, Andersen SU, Stougaard J, Ross L, Szczyglowski K. Lotus japonicus SUNERGOS1 encodes a predicted subunit A of a DNA topoisomerase VI that is required for nodule differentiation and accommodation of rhizobial infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:811-21. [PMID: 24661810 PMCID: PMC4282747 DOI: 10.1111/tpj.12520] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/13/2014] [Accepted: 03/05/2014] [Indexed: 05/05/2023]
Abstract
A symbiotic mutant of Lotus japonicus, called sunergos1-1 (suner1-1), originated from a har1-1 suppressor screen. suner1-1 supports epidermal infection by Mesorhizobium loti and initiates cell divisions for organogenesis of nodule primordia. However, these processes appear to be temporarily stalled early during symbiotic interaction, leading to a low nodule number phenotype. This defect is ephemeral and near wild-type nodule numbers are reached by suner1-1 at a later point after infection. Using an approach that combined map-based cloning and next-generation sequencing we have identified the causative mutation and show that the suner1-1 phenotype is determined by a weak recessive allele, with the corresponding wild-type SUNER1 locus encoding a predicted subunit A of a DNA topoisomerase VI. Our data suggest that at least one function of SUNER1 during symbiosis is to participate in endoreduplication, which is an essential step during normal differentiation of functional, nitrogen-fixing nodules.
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Affiliation(s)
- Hwi Joong Yoon
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research CentreLondon, ON, N5V 4T3, Canada
- Department of Biology, University of Western OntarioLondon, ON, N6A 5B7, Canada
| | - Md Shakhawat Hossain
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research CentreLondon, ON, N5V 4T3, Canada
| | - Mark Held
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research CentreLondon, ON, N5V 4T3, Canada
- Department of Biology, University of Western OntarioLondon, ON, N6A 5B7, Canada
| | - Hongwei Hou
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research CentreLondon, ON, N5V 4T3, Canada
| | - Marilyn Kehl
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research CentreLondon, ON, N5V 4T3, Canada
- Department of Biology, University of Western OntarioLondon, ON, N6A 5B7, Canada
| | - Alexandre Tromas
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research CentreLondon, ON, N5V 4T3, Canada
| | - Shusei Sato
- Kazusa DNA Research InstituteKisarazu, Chiba, 292-0812, Japan
| | - Satoshi Tabata
- Kazusa DNA Research InstituteKisarazu, Chiba, 292-0812, Japan
| | - Stig Uggerhøj Andersen
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus UniversityGustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus UniversityGustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Loretta Ross
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research CentreLondon, ON, N5V 4T3, Canada
| | - Krzysztof Szczyglowski
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research CentreLondon, ON, N5V 4T3, Canada
- Department of Biology, University of Western OntarioLondon, ON, N6A 5B7, Canada
- *For correspondence (e-mail )
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Suzaki T, Ito M, Yoro E, Sato S, Hirakawa H, Takeda N, Kawaguchi M. Endoreduplication-mediated initiation of symbiotic organ development in Lotus japonicus. Development 2014; 141:2441-5. [PMID: 24850853 DOI: 10.1242/dev.107946] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Many leguminous plants have a unique ability to reset and alter the fate of differentiated root cortical cells to form new organs of nitrogen-fixing root nodules during legume-Rhizobium symbiosis. Recent genetic studies on the role of cytokinin signaling reveal that activation of cytokinin signaling is crucial to the nodule organogenesis process. However, the genetic mechanism underlying the initiation of nodule organogenesis is poorly understood due to the low number of genes that have been identified. Here, we have identified a novel nodulation-deficient mutant named vagrant infection thread 1 (vag1) after suppressor mutant screening of spontaneous nodule formation 2, a cytokinin receptor gain-of-function mutant in Lotus japonicus. The VAG1 gene encodes a protein that is putatively orthologous to Arabidopsis ROOT HAIRLESS 1/HYPOCOTYL 7, a component of the plant DNA topoisomerase VI that is involved in the control of endoreduplication. Nodule phenotype of the vag1 mutant shows that VAG1 is required for the ploidy-dependent cell growth of rhizobial-infected cells. Furthermore, VAG1 mediates the onset of endoreduplication in cortical cells during early nodule development, which may be essential for the initiation of cortical cell proliferation that leads to nodule primordium formation. In addition, cortical infection is severely impaired in the vag1 mutants, whereas the epidermal infection threads formation is normal. This suggests that the VAG1-mediated endoreduplication of cortical cells may be required for the guidance of symbiotic bacteria to host meristematic cells.
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Affiliation(s)
- Takuya Suzaki
- National Institute for Basic Biology, Okazaki 444-8585, Japan School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Momoyo Ito
- National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Emiko Yoro
- National Institute for Basic Biology, Okazaki 444-8585, Japan School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | | | - Naoya Takeda
- National Institute for Basic Biology, Okazaki 444-8585, Japan School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Okazaki 444-8585, Japan School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
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Radicicol confers mid-schizont arrest by inhibiting mitochondrial replication in Plasmodium falciparum. Antimicrob Agents Chemother 2014; 58:4341-52. [PMID: 24841259 DOI: 10.1128/aac.02519-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Radicicol, an antifungal antibiotic, was previously identified as a compound having antimalarial activity. However, its mechanism of action in Plasmodium falciparum was not elucidated. While characterizing its antimalarial function, we observed that radicicol manifested two distinct developmental defects in cultured P. falciparum in a concentration-dependent manner. At a low concentration of radicicol, a significant percentage of drug-treated parasites were arrested at the schizont stage, while at a higher concentration, the parasites were unable to multiply from schizont to ring. Also, the newly formed rings and trophozoites were extremely delayed in development, eventually leading to cell death. We intended to characterize the potential molecular target of radicicol at its sublethal doses. Our results demonstrated that radicicol specifically impaired mitochondrial replication. This decrement was associated with a severalfold increment of the topoisomerase VIB transcript as well as protein in treated cells over that of untreated parasites. Topoisomerase VIB was found to be localized in the organelle fraction. Our docking study revealed that radicicol fits into the Bergerat fold of Pf topoisomerase VIB present in its ATPase domain. Altogether, these data allow us to conclude that P. falciparum topoisomerase VIB might be one of the targets of radicicol causing inhibition of mitochondrial replication. Hence, radicicol can be suitably employed to explore the mitochondrial physiology of malaria parasites.
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Guo J, Wu J, Zhang T, Gong H. Over-expression of SlCycA3 gene in Arabidopsis accelerated the cell cycle transition. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:659-670. [PMID: 32481021 DOI: 10.1071/fp13335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 12/18/2013] [Indexed: 06/11/2023]
Abstract
We characterised an A-type cyclin SlCycA3 (AJ243453) from tomato (Solanum lycopersicum L.). Phylogenetic analysis based on the deduced amino acid sequence revealed that SlCycA3 was 71% identical to A3-type cyclin in Nicotiana tabacum L. (CAA63540), 48% identical to its homologue found in Arabidopsis thaliana (NP_199122), and 48% identical to its homologue in Pisum sativum L. (CAB77269). SlCycA3 gene was transformed into Arabidopsis plants in order to study its function. The hypocotyl length of transgenic plants was approximately half the length of wild-type plants, and the cell size in the transgenic lines was also smaller. The transgenic plants had longer roots than the wild type. Overexpression of SlCycA3 gene accelerated the cell cycle from G1/S transition to early M-phase, thereby accelerating the cell division. When the plants were treated with IAA and 3-indolebutyric acid (IBA) for 2 days, the transgenic plants produced more lateral roots than wild type. Treatment with IBA significantly increased the cell number in the G2-phase in transgenic plants compared with wild type after treatment for 10 days, whereas the proportion of cells in the S-phase was strongly increased by IAA treatment both in wild-type and transgenic plants. These results suggest a possible key role for cyclin in regulating root growth and development and provide some evidence of cell division underlying hormone treatment in plants.
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Affiliation(s)
- Jia Guo
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiawen Wu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tiantian Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haijun Gong
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Takahashi M, Furuhashi T, Ishikawa N, Horiguchi G, Sakamoto A, Tsukaya H, Morikawa H. Nitrogen dioxide regulates organ growth by controlling cell proliferation and enlargement in Arabidopsis. THE NEW PHYTOLOGIST 2014; 201:1304-1315. [PMID: 24354517 DOI: 10.1111/nph.12609] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 10/20/2013] [Indexed: 05/08/2023]
Abstract
• To gain more insight into the physiological function of nitrogen dioxide (NO₂), we investigated the effects of exogenous NO₂ on growth in Arabidopsis thaliana. • Plants were grown in air without NO₂ for 1 wk after sowing and then grown for 1-4 wk in air with (designated treated plants) or without (control plants) NO₂. Plants were irrigated semiweekly with a nutrient solution containing 19.7 mM nitrate and 10.3 mM ammonium. • Five-week-old plants treated with 50 ppb NO₂ showed a ≤ 2.8-fold increase in biomass relative to controls. Treated plants also showed early flowering. The magnitude of the effects of NO₂ on leaf expansion, cell proliferation and enlargement was greater in developing than in maturing leaves. Leaf areas were 1.3-8.4 times larger on treated plants than corresponding leaves on control plants. The NO₂-induced increase in leaf size was largely attributable to cell proliferation in developing leaves, but was attributable to both cell proliferation and enlargement in maturing leaves. The expression of different sets of genes for cell proliferation and/or enlargement was induced by NO₂, but depended on the leaf developmental stage. • Collectively, these results indicated that NO₂ regulates organ growth by controlling cell proliferation and enlargement.
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Affiliation(s)
- Misa Takahashi
- Department of Mathematical and Life Sciences, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Takamasa Furuhashi
- Department of Mathematical and Life Sciences, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Naoko Ishikawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Atsushi Sakamoto
- Department of Mathematical and Life Sciences, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiromichi Morikawa
- Department of Mathematical and Life Sciences, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
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Gilkerson J, Callis J. A genetic screen for mutants defective in IAA1-LUC degradation in Arabidopsis thaliana reveals an important requirement for TOPOISOMERASE6B in auxin physiology. PLANT SIGNALING & BEHAVIOR 2014; 9:e972207. [PMID: 25482814 PMCID: PMC4622002 DOI: 10.4161/psb.29850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Many plant growth and developmental processes are modulated by the hormone auxin. Auxin-modulated proteolysis of Aux/IAAs, a family of transcriptional repressors, represents a major mode of auxin action. Auxin facilitates the interaction of Aux/IAAs with TIR1/AFB F-box proteins, promoting their ubiquitination by the SCF(TIR1/AFB) ubiquitin E3 ligase leading to subsequent degradation by the 26S proteasome. To identify new genes regulating Aux/IAA proteolysis in Arabidopsis thaliana, we took a genetic approach, identifying individuals with altered degradation of an IAA1-luciferase fusion protein (IAA1-LUC). A mutant with 2-fold slower IAA1-LUC degradation rate compared with wild-type was isolated. Positional cloning identified the mutant as an allele of TOPOISOMERASE6B, named top6b-7. TOP6B encodes a subunit of a plant and archea-specific enzyme regulating endoreduplication, DNA damage repair and transcription in plants. T-DNA insertion alleles (top6b-8 and top6b-9) were also analyzed. top6b-7 seedlings are less sensitive to exogenous auxin than wild-type siblings in primary root growth assays, and experiments with DR5:GUS. Additionally, top6b-7 seedlings have a 40% reduction in the amount of endogenous IAA. These data suggest that increased IAA1-LUC half-life in top6b-7 probably results from a combination of both lower endogenous IAA levels and reduced sensitivity to auxin.
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Affiliation(s)
- Jonathan Gilkerson
- Department of Molecular and Cellular Biology and Plant Biology Graduate Group; University of California; Davis, CA USA
- Current address: Plant Biology Laboratory; Howard Hughes Medical Institute; Salk Institute for Biological Studies; La Jolla, CA USA
| | - Judy Callis
- Department of Molecular and Cellular Biology and Plant Biology Graduate Group; University of California; Davis, CA USA
- Correspondence to: Judy Callis;
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Zabka A, Polit JT, Bernasińska J, Maszewski J. DNA topoisomerase II-dependent control of the cell cycle progression in root meristems of Allium cepa. Cell Biol Int 2013; 38:355-67. [PMID: 24302674 DOI: 10.1002/cbin.10211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/27/2013] [Indexed: 12/14/2022]
Abstract
The catalytic ability of DNA topoisomerases (Topo) to generate short-term DNA breaks allow these enzymes to play crucial functions in managing DNA topology during S-phase replication, transcription, and chromatin-remodelling processes required to achieve commitment for the onset and transition through mitosis. Our experiments on root meristem cells of onion (Allium cepa) were designed to gain insight into the contribution of Topo II to plant-specific progression throughout interphase and mitosis. Irrespective of the position of the cell in interphase, the immunofluorescence of Topo II revealed similar nuclear labelling pattern with well defined signals dispersed in the nucleoplasm and the cortical zone of the nucleolus. Only weak labelling was detected in metaphase and anaphase chromosomes. Experiments with two potent anti-Topo II agents, doxorubicin (DOX, an anthracycline) and a bisdioxopiperazine derivative, ICRF-193, suggest that the inhibition-mediated increase in Topo II immunofluorescence may represent a compensatory mechanism, by which an up-regulated expression of the enzyme tends to counteract the drug-induced loss of indispensable catalytic and relaxation functions. γ-H2AX immunolabelling seems to indicate that both DOX- and ICRF-193-induced alterations in cell cycle progression reflect primarily the activity of the G2/M DNA damage checkpoint. Our findings provide evidence for the plant-specific cell cycle control mechanism induced by Topo II inhibitors under DNA stress conditions.
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Affiliation(s)
- Aneta Zabka
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland
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Schrader A, Uhrig JF. MIDGET cooperates with COP1 and SPA1 to repress flowering in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2013; 8:25600. [PMID: 23857347 PMCID: PMC4002626 DOI: 10.4161/psb.25600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The life cycle of plants is strictly regulated by light, which directly influences the initiation of developmental programs such as photomorphogenesis of seedlings and induction of flowering. When environmental conditions are unsuitable, both processes are actively repressed by the action of COP1/SPA protein complexes which participate in ubiquitylation and subsequent degradation of transcription factors. We have shown recently that MIDGET (MID), a regulator of the TOPOISOMERASE VI complex, physically interacts with COP1 and is required for its function as suppressor of photomorphogenesis. Here we show that in Arabidopsis thaliana, the MID protein similarly plays a role in COP1/SPA1-controlled repression of flowering under short-day conditions.
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Schrader A, Welter B, Hulskamp M, Hoecker U, Uhrig JF. MIDGET connects COP1-dependent development with endoreduplication in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:67-79. [PMID: 23573936 DOI: 10.1111/tpj.12199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 04/02/2013] [Accepted: 04/07/2013] [Indexed: 05/03/2023]
Abstract
In Arabidopsis thaliana, loss of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) function leads to constitutive photomorphogenesis in the dark associated with inhibition of endoreduplication in the hypocotyl, and a post-germination growth arrest. MIDGET (MID), a component of the TOPOISOMERASE VI (TOPOVI) complex, is essential for endoreduplication and genome integrity in A. thaliana. Here we show that MID and COP1 interact in vitro and in vivo through the amino terminus of COP1. We further demonstrate that MID supports sub-nuclear accumulation of COP1. The MID protein is not degraded in a COP1-dependent fashion in darkness, and the phenotypes of single and double mutants prove that MID is not a target of COP1 but rather a necessary factor for proper COP1 activity with respect to both, control of COP1-dependent morphogenesis and regulation of endoreduplication. Our data provide evidence for a functional connection between COP1 and the TOPOVI in plants linking COP1-dependent development with the regulation of endoreduplication.
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Affiliation(s)
- Andrea Schrader
- University of Cologne, Botanical Institute III, Zuelpicher Str. 47b, 50674, Koeln, Germany
| | - Bastian Welter
- University of Cologne, Botanical Institute III, Zuelpicher Str. 47b, 50674, Koeln, Germany
| | - Martin Hulskamp
- University of Cologne, Botanical Institute III, Zuelpicher Str. 47b, 50674, Koeln, Germany
| | - Ute Hoecker
- University of Cologne, Botanical Institute II, Zuelpicher Str. 47b, 50674, Koeln, Germany
| | - Joachim F Uhrig
- University of Cologne, Botanical Institute III, Zuelpicher Str. 47b, 50674, Koeln, Germany
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Hisanaga T, Ferjani A, Horiguchi G, Ishikawa N, Fujikura U, Kubo M, Demura T, Fukuda H, Ishida T, Sugimoto K, Tsukaya H. The ATM-dependent DNA damage response acts as an upstream trigger for compensation in the fas1 mutation during Arabidopsis leaf development. PLANT PHYSIOLOGY 2013; 162:831-41. [PMID: 23616603 PMCID: PMC3668073 DOI: 10.1104/pp.113.216796] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/23/2013] [Indexed: 05/18/2023]
Abstract
During leaf development, a decrease in cell number often triggers an increase in cell size. This phenomenon, called compensation, suggests that some system coordinates cell proliferation and cell expansion, but how this is mediated at the molecular level is still unclear. The fugu2 mutants in Arabidopsis (Arabidopsis thaliana) exhibit typical compensation phenotypes. Here, we report that the FUGU2 gene encodes FASCIATA1 (FAS1), the p150 subunit of Chromatin Assembly Factor1. To uncover how the fas1 mutation induces compensation, we performed microarray analyses and found that many genes involved in the DNA damage response are up-regulated in fas1. Our genetic analysis further showed that activation of the DNA damage response and the accompanying decrease of cell number in fas1 depend on ATAXIA TELANGIECTASIA MUTATED (ATM) but not on ATM AND RAD3 RELATED. Kinematic analysis suggested that the delay in the cell cycle leads to a decrease in cell number in fas1 and that loss of ATM partially restores this phenotype. Consistently, both cell size phenotypes and high ploidy phenotypes of fas1 are also suppressed by atm, supporting that the ATM-dependent DNA damage response leads to these phenotypes. Altogether, these data suggest that the ATM-dependent DNA damage response acts as an upstream trigger in fas1 to delay the cell cycle and promote entry into the endocycle, resulting in compensated cell expansion.
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Noir S, Bömer M, Takahashi N, Ishida T, Tsui TL, Balbi V, Shanahan H, Sugimoto K, Devoto A. Jasmonate controls leaf growth by repressing cell proliferation and the onset of endoreduplication while maintaining a potential stand-by mode. PLANT PHYSIOLOGY 2013; 161:1930-51. [PMID: 23439917 PMCID: PMC3613466 DOI: 10.1104/pp.113.214908] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Phytohormones regulate plant growth from cell division to organ development. Jasmonates (JAs) are signaling molecules that have been implicated in stress-induced responses. However, they have also been shown to inhibit plant growth, but the mechanisms are not well understood. The effects of methyl jasmonate (MeJA) on leaf growth regulation were investigated in Arabidopsis (Arabidopsis thaliana) mutants altered in JA synthesis and perception, allene oxide synthase and coi1-16B (for coronatine insensitive1), respectively. We show that MeJA inhibits leaf growth through the JA receptor COI1 by reducing both cell number and size. Further investigations using flow cytometry analyses allowed us to evaluate ploidy levels and to monitor cell cycle progression in leaves and cotyledons of Arabidopsis and/or Nicotiana benthamiana at different stages of development. Additionally, a novel global transcription profiling analysis involving continuous treatment with MeJA was carried out to identify the molecular players whose expression is regulated during leaf development by this hormone and COI1. The results of these studies revealed that MeJA delays the switch from the mitotic cell cycle to the endoreduplication cycle, which accompanies cell expansion, in a COI1-dependent manner and inhibits the mitotic cycle itself, arresting cells in G1 phase prior to the S-phase transition. Significantly, we show that MeJA activates critical regulators of endoreduplication and affects the expression of key determinants of DNA replication. Our discoveries also suggest that MeJA may contribute to the maintenance of a cellular "stand-by mode" by keeping the expression of ribosomal genes at an elevated level. Finally, we propose a novel model for MeJA-regulated COI1-dependent leaf growth inhibition.
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39
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Sakamoto Y, Takagi S. LITTLE NUCLEI 1 and 4 regulate nuclear morphology in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2013; 54:622-33. [PMID: 23396599 DOI: 10.1093/pcp/pct031] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The morphology of plant nuclei varies among different species, organs, tissues and cell types. However, mechanisms and factors involved in the maintenance of nuclear morphology are poorly understood. Because nuclei retain their shapes even after cytoskeletal inhibitor treatments both in vivo and in vitro, we assumed involvement of the nuclear lamina, which plays a critical role in the regulation of nuclear morphology in animals. The crude nuclear lamina fraction isolated from Arabidopsis thaliana leaves was analyzed by mass spectrometry, and putative nuclear lamina proteins were identified. Among their T-DNA insertion lines, nuclei of little nuclei1 (linc1) and linc4 disruptants were more spherical than those of wild-type plants. Because A. thaliana harbors four LINC genes, we prepared all single and linc1/4 and linc2/3 double disruptants. In leaf epidermal cells, the circularity index of the nucleus in all linc disruptants except linc3 was significantly higher than that in the wild-type plants. The extent of the effects of LINC1 and/or LINC4 disruption was significantly higher than that of the effects of LINC2 disruption. The nuclear area was significantly smaller in the linc1, linc4 and linc1/4 disruptants than in the wild-type plants. Regardless of the defects in nuclear morphology, all linc disruptants exhibited a normal ploidy level. In interphase cells, LINC1 and LINC4 were mainly localized to the nuclear periphery, whereas LINC2 was in the nucleoplasm and LINC3 was detected in both regions. From prometaphase to anaphase in mitotic root tip cells, LINC1 was co-localized with chromosomes, whereas other LINCs were dispersed in the cytoplasm.
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Affiliation(s)
- Yuki Sakamoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho 1-1, Toyonaka, Osaka, 560-0043 Japan.
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40
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Taylor JA, Mitchenall LA, Rejzek M, Field RA, Maxwell A. Application of a novel microtitre plate-based assay for the discovery of new inhibitors of DNA gyrase and DNA topoisomerase VI. PLoS One 2013; 8:e58010. [PMID: 23469129 PMCID: PMC3582512 DOI: 10.1371/journal.pone.0058010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 01/29/2013] [Indexed: 01/15/2023] Open
Abstract
DNA topoisomerases are highly exploited targets for antimicrobial drugs. The spread of antibiotic resistance represents a significant threat to public health and necessitates the discovery of inhibitors that target topoisomerases in novel ways. However, the traditional assays for topoisomerase activity are not suitable for the high-throughput approaches necessary for drug discovery. In this study we validate a novel assay for screening topoisomerase inhibitors. A library of 960 compounds was screened against Escherichia coli DNA gyrase and archaeal Methanosarcina mazei DNA topoisomerase VI. Several novel inhibitors were identified for both enzymes, and subsequently characterised in vitro and in vivo. Inhibitors from the M. mazei topoisomerase VI screen were tested for their ability to inhibit Arabidopsis topoisomerase VI in planta. The data from this work present new options for antibiotic drug discovery and provide insight into the mechanism of topoisomerase VI.
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Affiliation(s)
- James A. Taylor
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Lesley A. Mitchenall
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Robert A. Field
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, United Kingdom
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41
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Jun SE, Okushima Y, Nam J, Umeda M, Kim GT. Kip-related protein 3 is required for control of endoreduplication in the shoot apical meristem and leaves of Arabidopsis. Mol Cells 2013; 35:47-53. [PMID: 23314608 PMCID: PMC3887850 DOI: 10.1007/s10059-013-2270-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 11/05/2012] [Accepted: 11/06/2012] [Indexed: 11/29/2022] Open
Abstract
The cell cycle plays an important role in the development and adaptation of multicellular organisms; specifically, it allows them to optimally adjust their architecture in response to environmental changes. Kip-related proteins (KRPs) are important negative regulators of cyclin-dependent kinases (CDKs), which positively control the cell cycle during plant development. The Arabidopsis genome possesses seven KRP genes with low sequence similarity and distinct expression patterns; however, why Arabidopsis needs seven KRP genes and how these genes function in cell cycle regulation are unknown. Here, we focused on the characterization of KRP3, which was found to have unique functions in the shoot apical meristem (SAM) and leaves. KRP3 protein was localized to the SAM, including the ground meristem and vascular tissues in the ground part of the SAM and cotyledons. In addition, KRP3 protein was stabilized when treated with MG132, an inhibitor of the 26S proteasome, indicating that the protein may be regulated by 26S proteasome-mediated protein degradation. KRP3-overexpressing (KRP3 OE) transgenic plants showed reduced organ size, serrated leaves, and reduced fertility. Interestingly, the KRP3 OE transgenic plants showed a significant reduction in the size of the SAM with alterations in cell arrangement. In addition, compared to the wild type, the KRP3 OE transgenic plants had a higher DNA ploidy level in the SAM and leaves. Taken together, our data suggest that KRP3 plays important regulatory roles in the cell cycle and endoreduplication in the SAM and leaves.
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Affiliation(s)
- Sang Eun Jun
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714,
Korea
| | | | - Jaesung Nam
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714,
Korea
| | | | - Gyung-Tae Kim
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714,
Korea
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42
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Matsunaga S, Katagiri Y, Nagashima Y, Sugiyama T, Hasegawa J, Hayashi K, Sakamoto T. New insights into the dynamics of plant cell nuclei and chromosomes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 305:253-301. [PMID: 23890384 DOI: 10.1016/b978-0-12-407695-2.00006-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The plant lamin-like protein NMCP/AtLINC and orthologues of the SUN-KASH complex across the nuclear envelope (NE) show the universality of nuclear structure in eukaryotes. However, depletion of components in the connection complex of the NE in plants does not induce severe defects, unlike in animals. Appearance of the Rabl configuration is not dependent on genome size in plant species. Topoisomerase II and condensin II are not essential for plant chromosome condensation. Plant endoreduplication shares several common characteristics with animals, including involvement of cyclin-dependent kinases and E2F transcription factors. Recent finding regarding endomitosis regulator GIG1 shed light on the suppression mechanism of endomitosis in plants. The robustness of plants, compared with animals, is reflected in their genome redundancy. Spatiotemporal functional analyses using chromophore-assisted light inactivation, super-resolution microscopy, and 4D (3D plus time) imaging will reveal new insights into plant nuclear and chromosomal dynamics.
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Affiliation(s)
- Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan.
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43
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Sanchez MDLP, Costas C, Sequeira-Mendes J, Gutierrez C. Regulating DNA replication in plants. Cold Spring Harb Perspect Biol 2012; 4:a010140. [PMID: 23209151 PMCID: PMC3504439 DOI: 10.1101/cshperspect.a010140] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chromosomal DNA replication in plants has requirements and constraints similar to those in other eukaryotes. However, some aspects are plant-specific. Studies of DNA replication control in plants, which have unique developmental strategies, can offer unparalleled opportunities of comparing regulatory processes with yeast and, particularly, metazoa to identify common trends and basic rules. In addition to the comparative molecular and biochemical studies, genomic studies in plants that started with Arabidopsis thaliana in the year 2000 have now expanded to several dozens of species. This, together with the applicability of genomic approaches and the availability of a large collection of mutants, underscores the enormous potential to study DNA replication control in a whole developing organism. Recent advances in this field with particular focus on the DNA replication proteins, the nature of replication origins and their epigenetic landscape, and the control of endoreplication will be reviewed.
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Affiliation(s)
- Maria de la Paz Sanchez
- Centro de Biologia Molecular "Severo Ochoa," CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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44
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de Almeida Engler J, Kyndt T, Vieira P, Van Cappelle E, Boudolf V, Sanchez V, Escobar C, De Veylder L, Engler G, Abad P, Gheysen G. CCS52 and DEL1 genes are key components of the endocycle in nematode-induced feeding sites. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:185-98. [PMID: 22640471 DOI: 10.1111/j.1365-313x.2012.05054.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The establishment of galls and syncytia as feeding sites induced by root-knot and cyst nematodes, respectively, involves a progressive increase in nuclear and cellular size. Here we describe the functional characterization of endocycle activators CCS52A, CCS52B and a repressor of the endocycle, DEL1, during two types of nematode feeding site development in Arabidopsis thaliana. In situ hybridization analysis showed that expression of CCS52A1 and CCS52B was strongly induced in galls and syncytia and DEL1 was stably but weakly expressed throughout feeding site development. Down-regulation and over-expression of CCS52 and DEL1 in Arabidopsis drastically affected giant cell and syncytium growth, resulting in restrained nematode development, illustrating the need for mitotic activity and endo-reduplication for feeding site maturation. Exploiting the mechanism of endo-reduplication may be envisaged as a strategy to control plant-parasitic nematodes.
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Affiliation(s)
- Janice de Almeida Engler
- Institut National de la Recherche Agronomique, UMR 1355 ISA/Centre National de la Recherche Scientifique, UMR 7254 ISA/Université de Nice-Sophia Antipolis, UMR ISA, 400 Route des Chappes, Sophia-Antipolis, France.
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45
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Integration of stress-related and reactive oxygen species-mediated signals by Topoisomerase VI in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2012; 109:16360-5. [PMID: 22988090 DOI: 10.1073/pnas.1202041109] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Environmental stress often leads to an increased production of reactive oxygen species that are involved in plastid-to-nucleus retrograde signaling. Soon after the release of singlet oxygen ((1)O(2)) in chloroplasts of the flu mutant of Arabidopsis, reprogramming of nuclear gene expression reveals a rapid transfer of signals from the plastid to the nucleus. We have identified extraplastidic signaling constituents involved in (1)O(2)-initiated plastid-to-nucleus signaling and nuclear gene activation after mutagenizing a flu line expressing the luciferase reporter gene under the control of the promoter of a (1)O(2)-responsive AAA-ATPase gene (At3g28580) and isolating second-site mutations that lead to a constitutive up-regulation of the reporter gene or abrogate its (1)O(2)-dependent up-regulation. One of these mutants, caa39, turned out to be a weak mutant allele of the Topoisomerase VI (Topo VI) A-subunit gene with a single amino acid substitution. Transcript profile analysis of flu and flu caa39 mutants revealed that Topo VI is necessary for the full activation of AAA-ATPase and a set of (1)O(2)-responsive transcripts in response to (1)O(2). Topo VI binds to the promoter of the AAA-ATPase and other (1)O(2)-responsive genes, and hence could directly regulate their expression. Under photoinhibitory stress conditions, which enhance the production of (1)O(2) and H(2)O(2), Topo VI regulates (1)O(2)-responsive and H(2)O(2)-responsive genes in a distinct manner. These results suggest that Topo VI acts as an integrator of multiple signals generated by reactive oxygen species formed in plants under adverse environmental conditions.
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46
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Sliwinska E, Mathur J, Bewley JD. Synchronously developing collet hairs in Arabidopsis thaliana provide an easily accessible system for studying nuclear movement and endoreduplication. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4165-78. [PMID: 22451725 DOI: 10.1093/jxb/ers099] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Early Arabidopsis thaliana seedling growth includes the highly synchronous development of hairs from every epidermal cell of the collet (the root-hypocotyl transition zone). The dynamics of collet hair growth, and accompanying nuclear movement and endoreduplication, were followed using a combination of different fluorescent probes for time-lapse imaging and flow cytometry. Using laser-scanning confocal microscopy on the double-transgenic Arabidopsis hybrid line NLS-GFP-GUS × YPM, there appeared to be a correlation between nuclear position and the cell tip during growth of the collet hair cells, as occurs in asynchronously developing root hairs. However, disruption of nuclear movement in the growing collet hairs using low concentrations of cytoskeletal inhibitors demonstrated that nuclear positioning close to the tip of the cell is not essential for tip-directed growth of the hair. Nuclear DNA content increases from 4C to 16C during development of the collet hairs. Following cessation of growth, nuclei moved to the base of the hairs and then their movement became asynchronous and limited. Co-visualization of RFP-highlighted prevacuolar vesicles and GFP-labelled nuclei showed that, whereas small vesicles allowed unimpeded nuclear movement within the hair, transient stops and directional reversals coincided with the presence of larger vesicles in close proximity to the nucleus. Arabidopsis collet hairs provide a robust, easily accessible, naturally synchronized population of single tip-growing cells that can be used as a model cell type for studying nuclear movement and endoreduplication.
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Affiliation(s)
- Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Plant Genetics and Biotechnology, University of Technology and Life Sciences, Kaliskiego Ave. 7, 85-789 Bydgoszcz, Poland.
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47
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Forterre P. Introduction and Historical Perspective. CANCER DRUG DISCOVERY AND DEVELOPMENT 2012. [DOI: 10.1007/978-1-4614-0323-4_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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48
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Wozny M, Schattat MH, Mathur N, Barton K, Mathur J. Color recovery after photoconversion of H2B::mEosFP allows detection of increased nuclear DNA content in developing plant cells. PLANT PHYSIOLOGY 2012; 158:95-106. [PMID: 22108524 PMCID: PMC3252088 DOI: 10.1104/pp.111.187062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/21/2011] [Indexed: 05/10/2023]
Abstract
Many higher plants are polysomatic whereby different cells possess variable amounts of nuclear DNA. The conditional triggering of endocycles results in higher nuclear DNA content (C value) that in some cases has been correlated to increased cell size. While numerous multicolored fluorescent protein (FP) probes have revealed the general behavior of the nucleus and intranuclear components, direct visualization and estimation of changes in nuclear-DNA content in live cells during their development has not been possible. Recently, monomeric Eos fluorescent protein (mEosFP) has emerged as a useful photoconvertible protein whose color changes irreversibly from a green to a red fluorescent form upon exposure to violet-blue light. The stability and irreversibility of red fluorescent mEosFP suggests that detection of green color recovery would be possible as fresh mEosFP is produced after photoconversion. Thus a ratiometric evaluation of the red and green forms of mEosFP following photoconversion could be used to estimate production of a core histone such as H2B during its concomitant synthesis with DNA in the synthesis phase of the cell cycle. Here we present proof of concept observations on transgenic tobacco (Nicotiana tabacum) Bright Yellow 2 cells and Arabidopsis (Arabidopsis thaliana) plants stably expressing H2B::mEosFP. In Arabidopsis seedlings an increase in green fluorescence is observed specifically in cells known to undergo endoreduplication. The detection of changes in nuclear DNA content by correlating color recovery of H2B::mEosFP after photoconversion is a novel approach involving a single FP. The method has potential for facilitating detailed investigations on conditions that favor increased cell size and the development of polysomaty in plants.
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Affiliation(s)
| | | | | | | | - Jaideep Mathur
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G2W1
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49
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Vos SM, Tretter EM, Schmidt BH, Berger JM. All tangled up: how cells direct, manage and exploit topoisomerase function. Nat Rev Mol Cell Biol 2011; 12:827-41. [PMID: 22108601 DOI: 10.1038/nrm3228] [Citation(s) in RCA: 471] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Topoisomerases are complex molecular machines that modulate DNA topology to maintain chromosome superstructure and integrity. Although capable of stand-alone activity in vitro, topoisomerases are frequently linked to larger pathways and systems that resolve specific DNA superstructures and intermediates arising from cellular processes such as DNA repair, transcription, replication and chromosome compaction. Topoisomerase activity is indispensible to cells, but requires the transient breakage of DNA strands. This property has been exploited, often for significant clinical benefit, by various exogenous agents that interfere with cell proliferation. Despite decades of study, surprising findings involving topoisomerases continue to emerge with respect to their cellular function, regulation and utility as therapeutic targets.
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Affiliation(s)
- Seychelle M Vos
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
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50
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De Veylder L, Larkin JC, Schnittger A. Molecular control and function of endoreplication in development and physiology. TRENDS IN PLANT SCIENCE 2011; 16:624-34. [PMID: 21889902 DOI: 10.1016/j.tplants.2011.07.001] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 07/19/2011] [Accepted: 07/21/2011] [Indexed: 05/03/2023]
Abstract
Endoreplication, also called endoreduplication, is a cell cycle variant of multicellular eukaryotes in which mitosis is skipped and cells repeatedly replicate their DNA, resulting in cellular polyploidy. In recent years, research results have shed light on the molecular mechanism of endoreplication control, but the function of this cell-cycle variant has remained elusive. However, new evidence is at last providing insight into the biological relevance of cellular polyploidy, demonstrating that endoreplication is essential for developmental processes, such as cell fate maintenance, and is a prominent response to physiological conditions, such as pathogen attack or DNA damage. Thus, endoreplication is being revealed as an important module in plant growth that contributes to the robustness of plant life.
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