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Kutashev K, Meschichi A, Reeck S, Fonseca A, Sartori K, White CI, Sicard A, Rosa S. Differences in RAD51 transcriptional response and cell cycle dynamics reveal varying sensitivity to DNA damage among Arabidopsis thaliana root cell types. THE NEW PHYTOLOGIST 2024; 243:966-980. [PMID: 38840557 DOI: 10.1111/nph.19875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/11/2024] [Indexed: 06/07/2024]
Abstract
Throughout their lifecycle, plants are subjected to DNA damage from various sources, both environmental and endogenous. Investigating the mechanisms of the DNA damage response (DDR) is essential to unravel how plants adapt to the changing environment, which can induce varying amounts of DNA damage. Using a combination of whole-mount single-molecule RNA fluorescence in situ hybridization (WM-smFISH) and plant cell cycle reporter lines, we investigated the transcriptional activation of a key homologous recombination (HR) gene, RAD51, in response to increasing amounts of DNA damage in Arabidopsis thaliana roots. The results uncover consistent variations in RAD51 transcriptional response and cell cycle arrest among distinct cell types and developmental zones. Furthermore, we demonstrate that DNA damage induced by genotoxic stress results in RAD51 transcription throughout the whole cell cycle, dissociating its traditional link with S/G2 phases. This work advances the current comprehension of DNA damage response in plants by demonstrating quantitative differences in DDR activation. In addition, it reveals new associations with the cell cycle and cell types, providing crucial insights for further studies of the broader response mechanisms in plants.
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Affiliation(s)
- Konstantin Kutashev
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Anis Meschichi
- Department of Biology, Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zürich, Zürich, 8092, Switzerland
| | - Svenja Reeck
- Department of Cell and Developmental Biology, John Innes Centre, Research Park, Norwich, NR4 7UH, UK
| | - Alejandro Fonseca
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Kevin Sartori
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Charles I White
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293, CNRS, U1103 INSERM, Clermont-Ferrand, 63001, France
| | - Adrien Sicard
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
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2
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Herbst J, Li QQ, De Veylder L. Mechanistic insights into DNA damage recognition and checkpoint control in plants. NATURE PLANTS 2024; 10:539-550. [PMID: 38503962 DOI: 10.1038/s41477-024-01652-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/18/2024] [Indexed: 03/21/2024]
Abstract
The plant DNA damage response (DDR) pathway safeguards genomic integrity by rapid recognition and repair of DNA lesions that, if unrepaired, may cause genome instability. Most frequently, DNA repair goes hand in hand with a transient cell cycle arrest, which allows cells to repair the DNA lesions before engaging in a mitotic event, but consequently also affects plant growth and yield. Through the identification of DDR proteins and cell cycle regulators that react to DNA double-strand breaks or replication defects, it has become clear that these proteins and regulators form highly interconnected networks. These networks operate at both the transcriptional and post-transcriptional levels and include liquid-liquid phase separation and epigenetic mechanisms. Strikingly, whereas the upstream DDR sensors and signalling components are well conserved across eukaryotes, some of the more downstream effectors are diverged in plants, probably to suit unique lifestyle features. Additionally, DDR components display functional diversity across ancient plant species, dicots and monocots. The observed resistance of DDR mutants towards aluminium toxicity, phosphate limitation and seed ageing indicates that gaining knowledge about the plant DDR may offer solutions to combat the effects of climate change and the associated risk for food security.
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Affiliation(s)
- Josephine Herbst
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Qian-Qian Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
- Center for Plant Systems Biology, VIB, Gent, Belgium.
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3
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Sotta N, Sakamoto T, Kamiya T, Tabata R, Yamaguchi K, Shigenobu S, Yamada M, Hasebe M, Sawa S, Fujiwara T. NAC103 mutation alleviates DNA damage in an Arabidopsis thaliana mutant sensitive to excess boron. FRONTIERS IN PLANT SCIENCE 2023; 14:1099816. [PMID: 37063182 PMCID: PMC10090426 DOI: 10.3389/fpls.2023.1099816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
Excess boron (B) is toxic to plants and thereby causes DNA damage and cell death in root meristems. However, the underlying mechanisms which link boron and DNA damage remain unclear. It has been reported that the rpt5a-6 mutant of the 26S proteasome is sensitive to excess boron, resulting in more frequent cell death in root meristem and reduced root elongation. In this study, we showed that a reduction in root growth in the rpt5a mutant in the presence of high boron levels is repressed by a mutation in NAC domain containing transcription factor NAC103, a substrate of the proteasome, which functions in the unfolded protein response pathway. The mutation in NAC103 alleviated excess-B-induced DNA damage and cell death in root meristems of the rpt5a mutant. Superoxide ( O 2 - ) staining with nitroblue tetrazolium revealed that boron stress causes O 2 - accumulation in root tips, which was higher in the rpt5a-6 mutant, whereas the accumulation was lower in the rpt5a-6 nac103-3 double mutant. Our work demonstrates the overall involvement of NAC103 in maintaining healthy root meristem under excess boron conditions in the absence of RPT5A proteasome subunit.
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Affiliation(s)
- Naoyuki Sotta
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Takehiro Kamiya
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryo Tabata
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Katsushi Yamaguchi
- National Institutes for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | - Shuji Shigenobu
- National Institutes for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan
| | - Masashi Yamada
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Mitsuyasu Hasebe
- National Institutes for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
- International Research Center for Agricultural & Environmental Biology, Kumamoto University, Kumamoto, Japan
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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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: 12] [Impact Index Per Article: 12.0] [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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Wang J, Moeen-ud-din M, Yin R, Yang S. ROS Homeostasis Involved in Dose-Dependent Responses of Arabidopsis Seedlings to Copper Toxicity. Genes (Basel) 2022; 14:11. [PMID: 36672752 PMCID: PMC9858908 DOI: 10.3390/genes14010011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/13/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
As an essential element in plant nutrition, copper (Cu) can promote or inhibit plant growth depending on its concentration. However, the dose-dependent effects of copper, particularly on DNA damage associated with reactive oxygen species (ROS) homeostasis, are much less understood. In this work, we analyzed the dual effect of Cu (5, 20, and 60 μM) on the reproductive performance of Arabidopsis plants. Whereas Cu5 promoted inflorescence initiation and increased kilo seed weight, two higher concentrations, Cu20 and Cu60, delayed inflorescence initiation and negatively affected silique size. Excess Cu also induced changes in cellular redox homeostasis, which was examined by in situ visualization and measurements of ROS, including superoxide (O2•-), hydrogen peroxide (H2O2), malonyldialdehyde (MDA), and plasma membrane damage. The most dramatic increases in the production of O2•- and H2O2 along with increased activity of superoxide dismutase (SOD) and glutathione peroxidase (GPX) and decreased activity of catalase (CAT) and ascorbate peroxidase (APX) were observed in roots with Cu60. Oxidative stress also modulated the expression levels of a number of genes involved in the DNA damage response (DDR), particularly those related to DNA repair. The Cu-induced chlorosis of Arabidopsis seedlings could be alleviated by exogenous addition of glutathione (GSH) and ascorbate (Asc), as the chlorophyll content was significantly increased. Overall, internal homeostasis ROS and the associated DDR pathway and the corresponding scavenging mechanisms play a central role in the response of Arabidopsis to oxidative stress induced by inhibitory Cu concentrations. Our results have shown, for the first time, that the biphasic responses of Arabidopsis seedlings to increasing Cu concentrations involve different DNA damage responses and oxidative reactions. They provide the basis for elucidating the network of Cu-induced DDR-related genes and the regulatory mechanism of the complex ROS production and scavenging system.
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Affiliation(s)
| | | | | | - Shaohui Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
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Fedoreyeva LI, Baranova EN, Chaban IA, Dilovarova TA, Vanyushin BF, Kononenko NV. Elongating Effect of the Peptide AEDL on the Root of Nicotiana tabacum under Salinity. PLANTS 2022; 11:plants11101352. [PMID: 35631778 PMCID: PMC9147445 DOI: 10.3390/plants11101352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/18/2022]
Abstract
The overall survival of a plant depends on the development, growth, and functioning of the roots. Root development and growth are not only genetically programmed but are constantly influenced by environmental factors, with the roots adapting to such changes. The peptide AEDL (alanine–glutamine acid–asparagine acid–leucine) at a concentration of 10−7 M had an elongating effect on the root cells of Nicotiana tabacum seedlings. The action of this peptide at such a low concentration is similar to that of peptide phytohormones. In the presence of 150 mM NaCl, a strong distortion in the development and architecture of the tobacco roots was observed. However, the combined presence of AEDL and NaCl resulted in normal root development. In the presence of AEDL, reactive oxygen species (ROS) were detected in the elongation and root hair zones of the roots. The ROS marker fluorescence intensity in plant cells grown with AEDL was much lower than that of plant cells grown without the peptide. Thus, AEDL protected the root tissue from damage by oxidative stress caused by the toxic effects of NaCl. Localization and accumulation of AEDL at the root were tissue-specific. Fluorescence microscopy showed that FITC-AEDL predominantly localized in the zones of elongation and root hairs, with insignificant localization in the meristem zone. AEDL induced a change in the structural organization of chromatin. Structural changes in chromatin caused significant changes in the expression of numerous genes associated with the development and differentiation of the root system. In the roots of tobacco seedlings grown in the presence of AEDL, the expression of WOX family genes decreased, and differentiation of stem cells increased, which led to root elongation. However, in the presence of NaCl, elongation of the tobacco root occurred via a different mechanism involving genes of the expansin family that weaken the cell wall in the elongation zone. Root elongation of plants is of fundamental importance in biology and is especially relevant to crop production as it can affect crop yields.
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Affiliation(s)
- Larisa I. Fedoreyeva
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
- Correspondence:
| | - Ekaterina N. Baranova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
- N.V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, Botanicheskaya 4, 127276 Moscow, Russia
| | - Inn A. Chaban
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
| | - Tatyana A. Dilovarova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
| | - Boris F. Vanyushin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Neonila V. Kononenko
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (E.N.B.); (I.A.C.); (T.A.D.); (B.F.V.); (N.V.K.)
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7
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Li M, Hou L, Zhang C, Yang W, Liu X, Zhao H, Pang X, Li Y. Genome-Wide Identification of Direct Targets of ZjVND7 Reveals the Putative Roles of Whole-Genome Duplication in Sour Jujube in Regulating Xylem Vessel Differentiation and Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:829765. [PMID: 35185994 PMCID: PMC8854171 DOI: 10.3389/fpls.2022.829765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/12/2022] [Indexed: 06/02/2023]
Abstract
The effects of whole-genome duplication span multiple levels. Previous study reported that the autotetraploid sour jujube exhibited superior drought tolerance than diploid. However, the difference in water transport system between diploids and autotetraploids and its mechanism remain unclear. Here, we found the number of xylem vessels and parenchyma cells in autotetraploid sour jujube increased to nearly twice that of diploid sour jujube, which may be closely related to the differences in xylem vessel differentiation-related ZjVND7 targets between the two ploidy types. Although the five enriched binding motifs are different, the most reliable motif in both diploid and autotetraploid sour jujube was CTTNAAG. Additionally, ZjVND7 targeted 236 and 321 genes in diploids and autotetraploids, respectively. More identified targeted genes of ZjVND7 were annotated to xylem development, secondary wall synthesis, cell death, cell division, and DNA endoreplication in autotetraploids than in diploids. SMR1 plays distinct roles in both proliferating and differentiated cells. Under drought stress, the binding signal of ZjVND7 to ZjSMR1 was stronger in autotetraploids than in diploids, and the fold-changes in the expression of ZjVND7 and ZjSMR1 were larger in the autotetraploids than in the diploids. These results suggested that the targeted regulation of ZjVND7 on ZjSMR1 may play valuable roles in autotetraploids in the response to drought stress. We hypothesized that the binding of ZjVND7 to ZjSMR1 might play a role in cell division and transdifferentiation from parenchyma cells to vessels in the xylem. This regulation could prolong the cell cycle and regulate endoreplication in response to drought stress and abscisic acid, which may be stronger in polyploids.
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Affiliation(s)
- Meng Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Lu Hou
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Chenxing Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Weicong Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Xinru Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Hanqing Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Yingyue Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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8
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Pedroza-Garcia JA, Xiang Y, De Veylder L. Cell cycle checkpoint control in response to DNA damage by environmental stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:490-507. [PMID: 34741364 DOI: 10.1111/tpj.15567] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Being sessile organisms, plants are ubiquitously exposed to stresses that can affect the DNA replication process or cause DNA damage. To cope with these problems, plants utilize DNA damage response (DDR) pathways, consisting of both highly conserved and plant-specific elements. As a part of this DDR, cell cycle checkpoint control mechanisms either pause the cell cycle, to allow DNA repair, or lead cells into differentiation or programmed cell death, to prevent the transmission of DNA errors in the organism through mitosis or to its offspring via meiosis. The two major DDR cell cycle checkpoints control either the replication process or the G2/M transition. The latter is largely overseen by the plant-specific SOG1 transcription factor, which drives the activity of cyclin-dependent kinase inhibitors and MYB3R proteins, which are rate limiting for the G2/M transition. By contrast, the replication checkpoint is controlled by different players, including the conserved kinase WEE1 and likely the transcriptional repressor RBR1. These checkpoint mechanisms are called upon during developmental processes, in retrograde signaling pathways, and in response to biotic and abiotic stresses, including metal toxicity, cold, salinity, and phosphate deficiency. Additionally, the recent expansion of research from Arabidopsis to other model plants has revealed species-specific aspects of the DDR. Overall, it is becoming evidently clear that the DNA damage checkpoint mechanisms represent an important aspect of the adaptation of plants to a changing environment, hence gaining more knowledge about this topic might be helpful to increase the resilience of plants to climate change.
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Affiliation(s)
- José Antonio Pedroza-Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
| | - Yanli Xiang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
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9
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Romeiro Motta M, Zhao X, Pastuglia M, Belcram K, Roodbarkelari F, Komaki M, Harashima H, Komaki S, Kumar M, Bulankova P, Heese M, Riha K, Bouchez D, Schnittger A. B1-type cyclins control microtubule organization during cell division in Arabidopsis. EMBO Rep 2022; 23:e53995. [PMID: 34882930 PMCID: PMC8728612 DOI: 10.15252/embr.202153995] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 11/09/2022] Open
Abstract
Flowering plants contain a large number of cyclin families, each containing multiple members, most of which have not been characterized to date. Here, we analyzed the role of the B1 subclass of mitotic cyclins in cell cycle control during Arabidopsis development. While we reveal CYCB1;5 to be a pseudogene, the remaining four members were found to be expressed in dividing cells. Mutant analyses showed a complex pattern of overlapping, development-specific requirements of B1-type cyclins with CYCB1;2 playing a central role. The double mutant cycb1;1 cycb1;2 is severely compromised in growth, yet viable beyond the seedling stage, hence representing a unique opportunity to study the function of B1-type cyclin activity at the organismic level. Immunolocalization of microtubules in cycb1;1 cycb1;2 and treating mutants with the microtubule drug oryzalin revealed a key role of B1-type cyclins in orchestrating mitotic microtubule networks. Subsequently, we identified the GAMMA-TUBULIN COMPLEX PROTEIN 3-INTERACTING PROTEIN 1 (GIP1/MOZART) as an in vitro substrate of B1-type cyclin complexes and further genetic analyses support a potential role in the regulation of GIP1 by CYCB1s.
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Affiliation(s)
| | - Xin’Ai Zhao
- Department of Developmental BiologyUniversity of HamburgHamburgGermany
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Martine Pastuglia
- Institute Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
| | - Katia Belcram
- Institute Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
| | | | - Maki Komaki
- Department of Developmental BiologyUniversity of HamburgHamburgGermany
| | - Hirofumi Harashima
- RIKEN Center for Sustainable Resource ScienceYokohamaJapan
- Present address:
Solution Research LaboratoryAS ONE CorporationKawasakiJapan
| | - Shinichiro Komaki
- Department of Developmental BiologyUniversity of HamburgHamburgGermany
- Nara Institute of Science and TechnologyNaraJapan
| | - Manoj Kumar
- Amity Institute of Genome EngineeringAmity University Uttar PradeshSector 125NoidaIndia
| | | | - Maren Heese
- Department of Developmental BiologyUniversity of HamburgHamburgGermany
| | - Karel Riha
- Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - David Bouchez
- Institute Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersaillesFrance
| | - Arp Schnittger
- Department of Developmental BiologyUniversity of HamburgHamburgGermany
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10
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Structural conservation of WEE1 and its role in cell cycle regulation in plants. Sci Rep 2021; 11:23862. [PMID: 34903771 PMCID: PMC8668995 DOI: 10.1038/s41598-021-03268-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/29/2021] [Indexed: 01/08/2023] Open
Abstract
The WEE1 kinase is ubiquitous in plant development and negatively regulates the cell cycle through phosphorylations. However, analogies with the control of the human cell cycle by tyrosine- (Tyr-) phosphorylation of cyclin-dependent kinases (CDKs) are sometimes questioned. In this in silico study, we assessed the structural conservation of the WEE1 protein in the plant kingdom with a particular focus on agronomically valuable plants, the legume crops. We analyzed the phylogenetic distribution of amino-acid sequences among a large number of plants by Bayesian analysis that highlighted the general conservation of WEE1 proteins. A detailed sequence analysis confirmed the catalytic potential of WEE1 proteins in plants. However, some substitutions of an arginine and a glutamate at the entrance of the catalytic pocket, illustrated by 3D structure predictions, challenged the specificity of this protein toward the substrate and Tyr-phosphorylation compared to the human WEE1. The structural differences, which could be responsible for the loss of specificity between human and plants, are highlighted and suggest the involvement of plant WEE1 in more cell regulation processes.
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11
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Zhao Y, Wang L, Sun X, Bao Y, Liu H, Zhao Y. Inhibition of ribosome biogenesis by actinomycin D affects Arabidopsis root development. Biochem Biophys Res Commun 2021; 588:61-67. [PMID: 34952471 DOI: 10.1016/j.bbrc.2021.12.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 12/14/2022]
Abstract
Actinomycin D has been reported to selectively inhibit rRNA synthesis and ribosome biogenesis, induce G2 checkpoint of cell cycle arrest in HeLa cells. In Arabidopsis, actinomycin D was also used as agent to preferentially inhibit the ribosome biosynthesis and ribosomal function. However, the function of actinomycin D on Arabidopsis root development remains to be elucidated. In this study, we exposed Arabidopsis seedlings to actinomycin D with the aim of evaluating the effects of ribosome biogenesis on root development. The results demonstrated that actinomycin D inhibited Arabidopsis root growth by reduced meristematic activity in a dose dependent manner. Exposure to actinomycin D decreased the expression of WOX5 and key stem cell niche-defining transcription factors SHR and PLT1, thus the loss function of QC identity and stem cell niche maintenance. In addition, dead cells were observed after actinomycin D treatment in root stele initials and DNA damage response was constitutively activated. Collectively, we propose that ribosome biogenesis plays key role in primary root growth through maintenance of root stem cell niche and DNA damage response in Arabidopsis.
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Affiliation(s)
- Yanxue Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, People's Republic of China
| | - Lei Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, People's Republic of China
| | - Xuwu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, People's Republic of China
| | - Yiqun Bao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Hao Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, People's Republic of China.
| | - Yanxue Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, People's Republic of China.
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12
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Takatsuka H, Shibata A, Umeda M. Genome Maintenance Mechanisms at the Chromatin Level. Int J Mol Sci 2021; 22:ijms221910384. [PMID: 34638727 PMCID: PMC8508675 DOI: 10.3390/ijms221910384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
Genome integrity is constantly threatened by internal and external stressors, in both animals and plants. As plants are sessile, a variety of environment stressors can damage their DNA. In the nucleus, DNA twines around histone proteins to form the higher-order structure “chromatin”. Unraveling how chromatin transforms on sensing genotoxic stress is, thus, key to understanding plant strategies to cope with fluctuating environments. In recent years, accumulating evidence in plant research has suggested that chromatin plays a crucial role in protecting DNA from genotoxic stress in three ways: (1) changes in chromatin modifications around damaged sites enhance DNA repair by providing a scaffold and/or easy access to DNA repair machinery; (2) DNA damage triggers genome-wide alterations in chromatin modifications, globally modulating gene expression required for DNA damage response, such as stem cell death, cell-cycle arrest, and an early onset of endoreplication; and (3) condensed chromatin functions as a physical barrier against genotoxic stressors to protect DNA. In this review, we highlight the chromatin-level control of genome stability and compare the regulatory systems in plants and animals to find out unique mechanisms maintaining genome integrity under genotoxic stress.
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Affiliation(s)
- Hirotomo Takatsuka
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-Machi, Kanazawa 920-1192, Japan;
| | - Atsushi Shibata
- Signal Transduction Program, Gunma University Initiative for Advanced Research (GIAR), 3-39-22, Showa-Machi, Maebashi 371-8511, Japan;
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
- Correspondence:
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13
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Gentric N, Genschik P, Noir S. Connections between the Cell Cycle and the DNA Damage Response in Plants. Int J Mol Sci 2021; 22:ijms22179558. [PMID: 34502465 PMCID: PMC8431409 DOI: 10.3390/ijms22179558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 12/02/2022] Open
Abstract
Due to their sessile lifestyle, plants are especially exposed to various stresses, including genotoxic stress, which results in altered genome integrity. Upon the detection of DNA damage, distinct cellular responses lead to cell cycle arrest and the induction of DNA repair mechanisms. Interestingly, it has been shown that some cell cycle regulators are not only required for meristem activity and plant development but are also key to cope with the occurrence of DNA lesions. In this review, we first summarize some important regulatory steps of the plant cell cycle and present a brief overview of the DNA damage response (DDR) mechanisms. Then, the role played by some cell cycle regulators at the interface between the cell cycle and DNA damage responses is discussed more specifically.
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14
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Pedroza-Garcia JA, Eekhout T, Achon I, Nisa MU, Coussens G, Vercauteren I, Van den Daele H, Pauwels L, Van Lijsebettens M, Raynaud C, De Veylder L. Maize ATR safeguards genome stability during kernel development to prevent early endosperm endocycle onset and cell death. THE PLANT CELL 2021; 33:2662-2684. [PMID: 34086963 PMCID: PMC8408457 DOI: 10.1093/plcell/koab158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/31/2021] [Indexed: 05/06/2023]
Abstract
The ataxia-telangiectasia mutated (ATM) and ATM and Rad3-related (ATR) kinases coordinate the DNA damage response. The roles described for Arabidopsis thaliana ATR and ATM are assumed to be conserved over other plant species, but molecular evidence is scarce. Here, we demonstrate that the functions of ATR and ATM are only partially conserved between Arabidopsis and maize (Zea mays). In both species, ATR and ATM play a key role in DNA repair and cell cycle checkpoint activation, but whereas Arabidopsis plants do not suffer from the absence of ATR under control growth conditions, maize mutant plants accumulate replication defects, likely due to their large genome size. Moreover, contrarily to Arabidopsis, maize ATM deficiency does not trigger meiotic defects, whereas the ATR kinase appears to be crucial for the maternal fertility. Strikingly, ATR is required to repress premature endocycle onset and cell death in the maize endosperm. Its absence results in a reduction of kernel size, protein and starch content, and a stochastic death of kernels, a process being counteracted by ATM. Additionally, while Arabidopsis atr atm double mutants are viable, no such mutants could be obtained for maize. Therefore, our data highlight that the mechanisms maintaining genome integrity may be more important for vegetative and reproductive development than previously anticipated.
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Affiliation(s)
- Jose Antonio Pedroza-Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ignacio Achon
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Maher-Un Nisa
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, Paris University, Sorbonne Paris-Cite, University of Paris-Saclay, 91405, Orsay, France
| | - Griet Coussens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Hilde Van den Daele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, Paris University, Sorbonne Paris-Cite, University of Paris-Saclay, 91405, Orsay, France
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15
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Eekhout T, Pedroza-Garcia JA, Kalhorzadeh P, De Jaeger G, De Veylder L. A Mutation in DNA Polymerase α Rescues WEE1KO Sensitivity to HU. Int J Mol Sci 2021; 22:9409. [PMID: 34502313 PMCID: PMC8430855 DOI: 10.3390/ijms22179409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
During DNA replication, the WEE1 kinase is responsible for safeguarding genomic integrity by phosphorylating and thus inhibiting cyclin-dependent kinases (CDKs), which are the driving force of the cell cycle. Consequentially, wee1 mutant plants fail to respond properly to problems arising during DNA replication and are hypersensitive to replication stress. Here, we report the identification of the polα-2 mutant, mutated in the catalytic subunit of DNA polymerase α, as a suppressor mutant of wee1. The mutated protein appears to be less stable, causing a loss of interaction with its subunits and resulting in a prolonged S-phase.
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Affiliation(s)
- Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium; (T.E.); (J.A.P.-G.); (P.K.); (G.D.J.)
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - José Antonio Pedroza-Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium; (T.E.); (J.A.P.-G.); (P.K.); (G.D.J.)
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Pooneh Kalhorzadeh
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium; (T.E.); (J.A.P.-G.); (P.K.); (G.D.J.)
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium; (T.E.); (J.A.P.-G.); (P.K.); (G.D.J.)
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium; (T.E.); (J.A.P.-G.); (P.K.); (G.D.J.)
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
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16
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Tulin F. Buying time: FASCIATA1 deficiency rescues wee1 plants from replication stress by delaying mitosis. PLANT PHYSIOLOGY 2021; 186:1762-1764. [PMID: 34618115 PMCID: PMC8331142 DOI: 10.1093/plphys/kiab256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Frej Tulin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
- Plant Science Department, Botany, Technische Universität München, 85354 Freising, Germany
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17
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Eekhout T, Dvorackova M, Pedroza Garcia JA, Nespor Dadejova M, Kalhorzadeh P, Van den Daele H, Vercauteren I, Fajkus J, De Veylder L. G2/M-checkpoint activation in fasciata1 rescues an aberrant S-phase checkpoint but causes genome instability. PLANT PHYSIOLOGY 2021; 186:1893-1907. [PMID: 34618100 PMCID: PMC8331141 DOI: 10.1093/plphys/kiab201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/05/2021] [Indexed: 05/13/2023]
Abstract
The WEE1 and ATM AND RAD3-RELATED (ATR) kinases are important regulators of the plant intra-S-phase checkpoint; consequently, WEE1KO and ATRKO roots are hypersensitive to replication-inhibitory drugs. Here, we report on a loss-of-function mutant allele of the FASCIATA1 (FAS1) subunit of the chromatin assembly factor 1 (CAF-1) complex that suppresses the phenotype of WEE1- or ATR-deficient Arabidopsis (Arabidopsis thaliana) plants. We demonstrate that lack of FAS1 activity results in the activation of an ATAXIA TELANGIECTASIA MUTATED (ATM)- and SUPPRESSOR OF GAMMA-RESPONSE 1 (SOG1)-mediated G2/M-arrest that renders the ATR and WEE1 checkpoint regulators redundant. This ATM activation accounts for the telomere erosion and loss of ribosomal DNA that are described for fas1 plants. Knocking out SOG1 in the fas1 wee1 background restores replication stress sensitivity, demonstrating that SOG1 is an important secondary checkpoint regulator in plants that fail to activate the intra-S-phase checkpoint.
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Affiliation(s)
- Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Martina Dvorackova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - José Antonio Pedroza Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Martina Nespor Dadejova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Pooneh Kalhorzadeh
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Hilde Van den Daele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Jiri Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
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18
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Lopez-Anido CB, Vatén A, Smoot NK, Sharma N, Guo V, Gong Y, Anleu Gil MX, Weimer AK, Bergmann DC. Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf. Dev Cell 2021; 56:1043-1055.e4. [PMID: 33823130 DOI: 10.1101/2020.09.08.288498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/19/2021] [Accepted: 03/09/2021] [Indexed: 05/22/2023]
Abstract
Dynamic cell identities underlie flexible developmental programs. The stomatal lineage in the Arabidopsis leaf epidermis features asynchronous and indeterminate divisions that can be modulated by environmental cues. The products of the lineage, stomatal guard cells and pavement cells, regulate plant-atmosphere exchanges, and the epidermis as a whole influences overall leaf growth. How flexibility is encoded in development of the stomatal lineage and how cell fates are coordinated in the leaf are open questions. Here, by leveraging single-cell transcriptomics and molecular genetics, we uncovered models of cell differentiation within Arabidopsis leaf tissue. Profiles across leaf tissues identified points of regulatory congruence. In the stomatal lineage, single-cell resolution resolved underlying cell heterogeneity within early stages and provided a fine-grained profile of guard cell differentiation. Through integration of genome-scale datasets and spatiotemporally precise functional manipulations, we also identified an extended role for the transcriptional regulator SPEECHLESS in reinforcing cell fate commitment.
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Affiliation(s)
- Camila B Lopez-Anido
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Anne Vatén
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Nicole K Smoot
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Nidhi Sharma
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Victoria Guo
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Yan Gong
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - M Ximena Anleu Gil
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA
| | - Annika K Weimer
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5020, USA.
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19
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Ye X, Huang HY, Wu FL, Cai LY, Lai NW, Deng CL, Guo JX, Yang LT, Chen LS. Molecular mechanisms for magnesium-deficiency-induced leaf vein lignification, enlargement and cracking in Citrus sinensis revealed by RNA-Seq. TREE PHYSIOLOGY 2021; 41:280-301. [PMID: 33104211 DOI: 10.1093/treephys/tpaa128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Citrus sinensis (L.) Osbeck seedlings were fertigated with nutrient solution containing 2 [magnesium (Mg)-sufficiency] or 0 mM (Mg-deficiency) Mg(NO3)2 for 16 weeks. Thereafter, RNA-Seq was used to investigate Mg-deficiency-responsive genes in the veins of upper and lower leaves in order to understand the molecular mechanisms for Mg-deficiency-induced vein lignification, enlargement and cracking, which appeared only in the lower leaves. In this study, 3065 upregulated and 1220 downregulated, and 1390 upregulated and 375 downregulated genes were identified in Mg-deficiency veins of lower leaves (MDVLL) vs Mg-sufficiency veins of lower leaves (MSVLL) and Mg-deficiency veins of upper leaves (MDVUL) vs Mg-sufficiency veins of upper leaves (MSVUL), respectively. There were 1473 common differentially expressed genes (DEGs) between MDVLL vs MSVLL and MDVUL vs MSVUL, 1463 of which displayed the same expression trend. Magnesium-deficiency-induced lignification, enlargement and cracking in veins of lower leaves might be related to the following factors: (i) numerous transciption factors and genes involved in lignin biosynthesis pathways, regulation of cell cycle and cell wall metabolism were upregulated; and (ii) reactive oxygen species, phytohormone and cell wall integrity signalings were activated. Conjoint analysis of proteome and transcriptome indicated that there were 287 and 56 common elements between DEGs and differentially abundant proteins (DAPs) identified in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, and that among these common elements, the abundances of 198 and 55 DAPs matched well with the transcript levels of the corresponding DEGs in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, indicating the existence of concordances between protein and transcript levels.
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Affiliation(s)
- Xin Ye
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Hui-Yu Huang
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Feng-Lin Wu
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Li-Ya Cai
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Ning-Wei Lai
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Chong-Ling Deng
- Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, 40 Putuo Road, Qixing District, Guilin 541004, China
| | - Jiu-Xin Guo
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Lin-Tong Yang
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Li-Song Chen
- Institute of Plant Nutritional Physiology and Molecular Biology, Department of Resources and Environment, College of Resources and Environment, Fujian Agriculture and Forestry University (FAFU), 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China
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20
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Kantharaj V, Ramasamy NK, Yoon YE, Cheong MS, Kim YN, Lee KA, Kumar V, Choe H, Kim SY, Chohra H, Lee YB. Auxin-Glucose Conjugation Protects the Rice ( Oryza sativa L.) Seedlings Against Hydroxyurea-Induced Phytotoxicity by Activating UDP-Glucosyltransferase Enzyme. FRONTIERS IN PLANT SCIENCE 2021; 12:767044. [PMID: 35251058 PMCID: PMC8888425 DOI: 10.3389/fpls.2021.767044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/27/2021] [Indexed: 05/02/2023]
Abstract
Hydroxyurea (HU) is the replication stress known to carry out cell cycle arrest by inhibiting ribonucleotide reductase (RNR) enzyme upon generating excess hydrogen peroxide (H2O2) in plants. Phytohormones undergo synergistic and antagonistic interactions with reactive oxygen species (ROS) and redox signaling to protect plants against biotic and abiotic stress. Therefore, in this study, we investigated the protective role of Indole-3-acetic acid (IAA) in mitigating HU-induced toxicity in rice seedlings. The results showed that IAA augmentation improved the growth of the seedlings and biomass production by maintaining photosynthesis metabolism under HU stress. This was associated with reduced H2O2 and malondialdehyde (MDA) contents and improved antioxidant enzyme [superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT), and peroxidase (POD)] activity that was significantly affected under HU stress. Furthermore, we showed that the HU stress-induced DNA damage leads to the activation of uridine 5'-diphosphate-glucosyltransferase (UGT), which mediates auxin homeostasis by catalyzing IAA-glucose conjugation in rice. This IAA-glucose conjugation upregulates the RNR, transcription factor 2 (E2F2), cyclin-dependent kinase (CDK), and cyclin (CYC) genes that are vital for DNA replication and cell division. As a result, perturbed IAA homeostasis significantly enhanced the key phytohormones, such as abscisic acid (ABA), salicylic acid (SA), cytokinin (CTK), and gibberellic acid (GA), that alter plant architecture by improving growth and development. Collectively, our results contribute to a better understanding of the physiological and molecular mechanisms underpinning improved growth following the HU + IAA combination, activated by phytohormone and ROS crosstalk upon hormone conjugation via UGT.
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Affiliation(s)
- Vimalraj Kantharaj
- Division of Applied Life Science (BK 21 Four), Gyeongsang National University, Jinju, South Korea
| | | | - Young-Eun Yoon
- Division of Applied Life Science (BK 21 Four), Gyeongsang National University, Jinju, South Korea
| | - Mi Sun Cheong
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Young-Nam Kim
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | - Keum-Ah Lee
- Department of Smart Agro-Industry, Gyeongsang National University, Jinju, South Korea
| | - Vikranth Kumar
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Hyeonji Choe
- Division of Applied Life Science (BK 21 Four), Gyeongsang National University, Jinju, South Korea
| | - Song Yeob Kim
- Division of Applied Life Science (BK 21 Four), Gyeongsang National University, Jinju, South Korea
| | - Hadjer Chohra
- Division of Applied Life Science (BK 21 Four), Gyeongsang National University, Jinju, South Korea
| | - Yong Bok Lee
- Division of Applied Life Science (BK 21 Four), Gyeongsang National University, Jinju, South Korea
- *Correspondence: Yong Bok Lee,
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21
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Bertels J, Huybrechts M, Hendrix S, Bervoets L, Cuypers A, Beemster GTS. Cadmium inhibits cell cycle progression and specifically accumulates in the maize leaf meristem. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6418-6428. [PMID: 32822498 DOI: 10.1093/jxb/eraa385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
It is well known that cadmium (Cd) pollution inhibits plant growth, but how this metal impacts leaf growth processes at the cellular and molecular level is still largely unknown. In the current study, we show that Cd specifically accumulates in the meristematic tissue of the growing maize leaf, while Cd concentration in the elongation zone rapidly declines as the deposition rates diminish and cell volumes increase due to cell expansion. A kinematic analysis shows that, at the cellular level, a lower number of meristematic cells together with a significantly longer cell cycle duration explain the inhibition of leaf growth by Cd. Flow cytometry analysis suggests an inhibition of the G1/S transition, resulting in a lower proportion of cells in the S phase and reduced endoreduplication in expanding cells under Cd stress. Lower cell cycle activity is also reflected by lower expression levels of key cell cycle genes (putative wee1, cyclin-B2-4, and minichromosome maintenance4). Cell elongation rates are also inhibited by Cd, which is possibly linked to the inhibited endoreduplication. Taken together, our results complement studies on Cd-induced growth inhibition in roots and link inhibited cell cycle progression to Cd deposition in the leaf meristem.
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Affiliation(s)
- Jonas Bertels
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), University of Antwerp, Groenenborgerlaan, Antwerpen, Belgium
| | - Michiel Huybrechts
- Centre for Environmental Sciences (CMK), Hasselt University, Agoralaan Building D, Diepenbeek, Belgium
| | - Sophie Hendrix
- Centre for Environmental Sciences (CMK), Hasselt University, Agoralaan Building D, Diepenbeek, Belgium
| | - Lieven Bervoets
- Systemic Physiological and Ecotoxicological Research (SPHERE), University of Antwerp, Groenenborgerlaan, Antwerpen, Belgium
| | - Ann Cuypers
- Centre for Environmental Sciences (CMK), Hasselt University, Agoralaan Building D, Diepenbeek, Belgium
| | - Gerrit T S Beemster
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), University of Antwerp, Groenenborgerlaan, Antwerpen, Belgium
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Żabka A, Winnicki K, Polit JT, Bernasińska-Słomczewska J, Maszewski J. 5-Aminouracil and other inhibitors of DNA replication induce biphasic interphase-mitotic cells in apical root meristems of Allium cepa. PLANT CELL REPORTS 2020; 39:1013-1028. [PMID: 32328702 PMCID: PMC7359111 DOI: 10.1007/s00299-020-02545-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Induction of biphasic interphase-mitotic cells and PCC is connected with an increased level of metabolism in root meristem cells of Allium cepa. Previous experiments using primary roots of Allium cepa exposed to low concentrations of hydroxyurea have shown that long-term DNA replication stress (DRS) disrupts essential links of the S-M checkpoint mechanism, leading meristem cells either to premature chromosome condensation (PCC) or to a specific form of chromatin condensation, establishing biphasic organization of cell nuclei with both interphase and mitotic domains (IM cells). The present study supplements and extends these observations by describing general conditions under which both abnormal types of M-phase cells may occur. The analysis of root apical meristem (RAM) cell proliferation after prolonged mild DRS indicates that a broad spectrum of inhibitors is capable of generating PCC and IM organization of cell nuclei. These included: 5-aminouracil (5-AU, a thymine antagonist), characterized by the highest efficiency in creating cells with the IM phenotype, aphidicolin (APH), an inhibitor of DNA polymerase α, 5-fluorodeoxyuridine (FUdR), an inhibitor of thymidylate synthetase, methotrexate (MTX), a folic acid analog that inhibits purine and pyrimidine synthesis, and cytosine arabinoside (Ara-C), which inhibits DNA replication by forming cleavage complexes with topoisomerase I. As evidenced using fluorescence-based click chemistry assays, continuous treatment of onion RAM cells with 5-AU is associated with an accelerated dynamics of the DNA replication machinery and significantly enhanced levels of transcription and translation. Furthermore, DRS conditions bring about an intensified production of hydrogen peroxide (H2O2), depletion of reduced glutathione (GSH), and some increase in DNA fragmentation, associated with only a slight increase in apoptosis-like programmed cell death events.
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Affiliation(s)
- Aneta Żabka
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Konrad Winnicki
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Justyna Teresa Polit
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Joanna Bernasińska-Słomczewska
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Janusz Maszewski
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
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23
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Lang L, Schnittger A. Endoreplication - a means to an end in cell growth and stress response. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:85-92. [PMID: 32217456 DOI: 10.1016/j.pbi.2020.02.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
Endoreplication, also called endoreduplication or endopolyploidization, is a cell cycle variant in which the genome is re-replicated in the absence of mitosis causing cellular polyploidization. Despite the common occurrence of endoreplication in plants and the tremendous extent in specific tissues and cell types such as the endosperm, the underlying molecular regulation and the physiological consequences have only now started to be understood. Endoreplication is often associated with cell differentiation and withdrawal from mitotic cycles. Recent studies have underlined the importance of endoreplication as a stress response and we summarize here this progress with particular focus on future perspectives offered by the recent advances in genomics and biotechnology.
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Affiliation(s)
- Lucas Lang
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Developmental Biology, Ohnhorststr. 18, D-22609 Hamburg, Germany
| | - Arp Schnittger
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Developmental Biology, Ohnhorststr. 18, D-22609 Hamburg, Germany.
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24
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Re-activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing. Cell 2020; 177:957-969.e13. [PMID: 31051107 PMCID: PMC6506278 DOI: 10.1016/j.cell.2019.04.015] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/18/2018] [Accepted: 04/07/2019] [Indexed: 11/23/2022]
Abstract
Patterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing.
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25
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Molecular Changes Concomitant with Vascular System Development in Mature Galls Induced by Root-Knot Nematodes in the Model Tree Host Populus tremula × P. alba. Int J Mol Sci 2020; 21:ijms21020406. [PMID: 31936440 PMCID: PMC7013992 DOI: 10.3390/ijms21020406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 12/22/2022] Open
Abstract
One of the most striking features occurring in the root-knot nematode Meloidogyne incognita induced galls is the reorganization of the vascular tissues. During the interaction of the model tree species Populus and M. incognita, a pronounced xylem proliferation was previously described in mature galls. To better characterise changes in expression of genes possibly involved in the induction and the formation of the de novo developed vascular tissues occurring in poplar galls, a comparative transcript profiling of 21-day-old galls versus uninfected root of poplar was performed. Genes coding for transcription factors associated with procambium maintenance and vascular differentiation were shown to be differentially regulated, together with genes partaking in phytohormones biosynthesis and signalling. Specific signatures of transcripts associated to primary cell wall biosynthesis and remodelling, as well as secondary cell wall formation (cellulose, xylan and lignin) were revealed in the galls. Ultimately, we show that molecules derived from the monolignol and salicylic acid pathways and related to secondary cell wall deposition accumulate in mature galls.
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26
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Cabral D, Banora MY, Antonino JD, Rodiuc N, Vieira P, Coelho RR, Chevalier C, Eekhout T, Engler G, De Veylder L, Grossi-de-Sa MF, de Almeida Engler J. The plant WEE1 kinase is involved in checkpoint control activation in nematode-induced galls. THE NEW PHYTOLOGIST 2020; 225:430-447. [PMID: 31505035 DOI: 10.1111/nph.16185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/15/2019] [Indexed: 06/10/2023]
Abstract
Galls induced by plant-parasitic nematodes involve a hyperactivation of the plant mitotic and endocycle machinery for their profit. Dedifferentiation of host root cells includes drastic cellular and molecular readjustments. In such a background, potential DNA damage in the genome of gall cells is evident. We investigated whether DNA damage checkpoint activation followed by DNA repair occurred, or was eventually circumvented, in nematode-induced galls. Galls display transcriptional activation of the DNA damage checkpoint kinase WEE1, correlated with its protein localization in the nuclei. The promoter of the stress marker gene SMR7 was evaluated under the WEE1-knockout background. Drugs inducing DNA damage and a marker for DNA repair, PARP1, were used to understand the mechanisms for coping with DNA damage in galls. Our functional study revealed that gall cells lacking WEE1 conceivably entered mitosis prematurely, disturbing the cell cycle despite the loss of genome integrity. The disrupted nuclei phenotype in giant cells hinted at the accumulation of mitotic defects. In addition, WEE1-knockout in Arabidopsis and downregulation in tomato repressed infection and reproduction of root-knot nematodes. Together with data on DNA-damaging drugs, we suggest a conserved function for WEE1 in controlling G1/S cell cycle arrest in response to a replication defect in galls.
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Affiliation(s)
- Danila Cabral
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Mohamed Youssef Banora
- Department of Plant Pathology, Faculty of Agriculture, Ain Shams University, PO Box 68, Hadayek Shoubra, 11241, Cairo, Egypt
- Department of Biology, Faculty of Science and Art-Khulais, University of Jeddah, Saudi Arabia
| | - José Dijair Antonino
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB, Av. W5 Norte Final, Brasília, DF, 70770-900, Brazil
- Departamento de Agronomia/Entomologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros S/N, Dois Irmãos,, Recife, PE, 521171-900, Brazil
| | - Natalia Rodiuc
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB, Av. W5 Norte Final, Brasília, DF, 70770-900, Brazil
| | - Paulo Vieira
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Roberta R Coelho
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB, Av. W5 Norte Final, Brasília, DF, 70770-900, Brazil
| | - Christian Chevalier
- UMR1332 BFP, INRA, University of Bordeaux, 33882, Villenave d'Ornon Cedex, France
| | - Thomas Eekhout
- Department of Plant Biotechnology and Genetics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Gilbert Engler
- INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Lieven De Veylder
- Department of Plant Biotechnology and Genetics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Maria Fatima Grossi-de-Sa
- Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB, Av. W5 Norte Final, Brasília, DF, 70770-900, Brazil
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27
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Waterworth WM, Wilson M, Wang D, Nuhse T, Warward S, Selley J, West CE. Phosphoproteomic analysis reveals plant DNA damage signalling pathways with a functional role for histone H2AX phosphorylation in plant growth under genotoxic stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1007-1021. [PMID: 31410901 PMCID: PMC6900162 DOI: 10.1111/tpj.14495] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 05/23/2023]
Abstract
DNA damage responses are crucial for plant growth under genotoxic stress. Accumulating evidence indicates that DNA damage responses differ between plant cell types. Here, quantitative shotgun phosphoproteomics provided high-throughput analysis of the DNA damage response network in callus cells. MS analysis revealed a wide network of highly dynamic changes in the phosphoprotein profile of genotoxin-treated cells, largely mediated by the ATAXIA TELANGIECTASIA MUTATED (ATM) protein kinase, representing candidate factors that modulate plant growth, development and DNA repair. A C-terminal dual serine target motif unique to H2AX in the plant lineage showed 171-fold phosphorylation that was absent in atm mutant lines. The physiological significance of post-translational DNA damage signalling to plant growth and survival was demonstrated using reverse genetics and complementation studies of h2ax mutants, establishing the functional role of ATM-mediated histone modification in plant growth under genotoxic stress. Our findings demonstrate the complexity and functional significance of post-translational DNA damage signalling responses in plants and establish the requirement of H2AX phosphorylation for plant survival under genotoxic stress.
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Affiliation(s)
| | - Michael Wilson
- Centre for Plant SciencesUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Dapeng Wang
- Leeds OmicsUniversity of LeedsLeedsLS2 9JTUK
| | - Thomas Nuhse
- Faculty of Life SciencesUniversity of ManchesterOxford RoadManchesterM13 9PTUK
| | - Stacey Warward
- Faculty of Life SciencesUniversity of ManchesterOxford RoadManchesterM13 9PTUK
| | - Julian Selley
- Faculty of Life SciencesUniversity of ManchesterOxford RoadManchesterM13 9PTUK
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28
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Olszak M, Truman W, Stefanowicz K, Sliwinska E, Ito M, Walerowski P, Rolfe S, Malinowski R. Transcriptional profiling identifies critical steps of cell cycle reprogramming necessary for Plasmodiophora brassicae-driven gall formation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:715-729. [PMID: 30431210 PMCID: PMC6850046 DOI: 10.1111/tpj.14156] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/31/2018] [Accepted: 11/06/2018] [Indexed: 05/08/2023]
Abstract
Plasmodiophora brassicae is a soil-borne biotroph whose life cycle involves reprogramming host developmental processes leading to the formation of galls on its underground parts. Formation of such structures involves modification of the host cell cycle leading initially to hyperplasia, increasing the number of cells to be invaded, followed by overgrowth of cells colonised by the pathogen. Here we show that P. brassicae infection stimulates formation of the E2Fa/RBR1 complex and upregulation of MYB3R1, MYB3R4 and A- and B-type cyclin expression. These factors were previously described as important regulators of the G2-M cell cycle checkpoint. As a consequence of this manipulation, a large population of host hypocotyl cells are delayed in cell cycle exit and maintained in the proliferative state. We also report that, during further maturation of galls, enlargement of host cells invaded by the pathogen involves endoreduplication leading to increased ploidy levels. This study characterises two aspects of the cell cycle reprogramming efforts of P. brassicae: systemic, related to the disturbance of host hypocotyl developmental programs by preventing cell cycle exit; and local, related to the stimulation of cell enlargement via increased endocycle activity.
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Affiliation(s)
- Marcin Olszak
- Department of Integrative Plant BiologyInstitute of Plant Genetics of the Polish Academy of Sciencesul. Strzeszyńska 3460‐479PoznańPoland
| | - William Truman
- Department of Integrative Plant BiologyInstitute of Plant Genetics of the Polish Academy of Sciencesul. Strzeszyńska 3460‐479PoznańPoland
| | - Karolina Stefanowicz
- Department of Integrative Plant BiologyInstitute of Plant Genetics of the Polish Academy of Sciencesul. Strzeszyńska 3460‐479PoznańPoland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and CytometryDepartment of Plant Genetics, Physiology and BiotechnologyUTP University of Science and TechnologyKaliskiego Ave. 785‐789BydgoszczPoland
| | - Masaki Ito
- Graduate School of Bioagricultural SciencesNagoya UniversityChikusaNagoya464‐8601Japan
| | - Piotr Walerowski
- Department of Integrative Plant BiologyInstitute of Plant Genetics of the Polish Academy of Sciencesul. Strzeszyńska 3460‐479PoznańPoland
| | - Stephen Rolfe
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldS10 2TNUK
| | - Robert Malinowski
- Department of Integrative Plant BiologyInstitute of Plant Genetics of the Polish Academy of Sciencesul. Strzeszyńska 3460‐479PoznańPoland
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29
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Nisa MU, Huang Y, Benhamed M, Raynaud C. The Plant DNA Damage Response: Signaling Pathways Leading to Growth Inhibition and Putative Role in Response to Stress Conditions. FRONTIERS IN PLANT SCIENCE 2019; 10:653. [PMID: 31164899 PMCID: PMC6534066 DOI: 10.3389/fpls.2019.00653] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/30/2019] [Indexed: 05/02/2023]
Abstract
Maintenance of genome integrity is a key issue for all living organisms. Cells are constantly exposed to DNA damage due to replication or transcription, cellular metabolic activities leading to the production of Reactive Oxygen Species (ROS) or even exposure to DNA damaging agents such as UV light. However, genomes remain extremely stable, thanks to the permanent repair of DNA lesions. One key mechanism contributing to genome stability is the DNA Damage Response (DDR) that activates DNA repair pathways, and in the case of proliferating cells, stops cell division until DNA repair is complete. The signaling mechanisms of the DDR are quite well conserved between organisms including in plants where they have been investigated into detail over the past 20 years. In this review we summarize the acquired knowledge and recent advances regarding the DDR control of cell cycle progression. Studying the plant DDR is particularly interesting because of their mode of development and lifestyle. Indeed, plants develop largely post-embryonically, and form new organs through the activity of meristems in which cells retain the ability to proliferate. In addition, they are sessile organisms that are permanently exposed to adverse conditions that could potentially induce DNA damage in all cell types including meristems. In the second part of the review we discuss the recent findings connecting the plant DDR to responses to biotic and abiotic stresses.
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30
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Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators. PLoS Genet 2018; 14:e1007797. [PMID: 30500810 PMCID: PMC6268010 DOI: 10.1371/journal.pgen.1007797] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/30/2018] [Indexed: 01/06/2023] Open
Abstract
Retinoblastoma (pRb) is a multifunctional regulator, which was likely present in the last common ancestor of all eukaryotes. The Arabidopsis pRb homolog RETINOBLASTOMA RELATED 1 (RBR1), similar to its animal counterparts, controls not only cell proliferation but is also implicated in developmental decisions, stress responses and maintenance of genome integrity. Although most functions of pRb-type proteins involve chromatin association, a genome-wide understanding of RBR1 binding sites in Arabidopsis is still missing. Here, we present a plant chromatin immunoprecipitation protocol optimized for genome-wide studies of indirectly DNA-bound proteins like RBR1. Our analysis revealed binding of Arabidopsis RBR1 to approximately 1000 genes and roughly 500 transposable elements, preferentially MITES. The RBR1-decorated genes broadly overlap with previously identified targets of two major transcription factors controlling the cell cycle, i.e. E2F and MYB3R3 and represent a robust inventory of RBR1-targets in dividing cells. Consistently, enriched motifs in the RBR1-marked domains include sequences related to the E2F consensus site and the MSA-core element bound by MYB3R transcription factors. Following up a key role of RBR1 in DNA damage response, we performed a meta-analysis combining the information about the RBR1-binding sites with genome-wide expression studies under DNA stress. As a result, we present the identification and mutant characterization of three novel genes required for growth upon genotoxic stress. The Retinoblastoma (pRb) tumor suppressor is a master regulator of the cell cycle and its inactivation is associated with many types of cancer. Since pRb’s first description as a transcriptional repressor of genes important for cell cycle progression, many more functions have been elucidated, e.g. in developmental decisions and genome integrity. Homologs of human pRb have been identified in most eukaryotes, including plants, indicating an ancient evolutionary origin of pRb-type proteins. We describe here the first genome-wide DNA-binding study for a plant pRb protein, i.e. RBR1, the only pRb homolog in Arabidopsis thaliana. We see prominent binding of RBR1 to the 5’ region of genes involved in cell cycle regulation, chromatin organization and DNA repair. Moreover, we also reveal extensive binding of RBR1 to specific classes of DNA transposons. Since RBR1 is involved in a plethora of processes, our dataset provides a valuable resource for researches from different fields. As an example, we used our dataset to successfully identify new genes necessary for growth upon DNA damage exerted by drugs such as cisplatin or the environmentally prevalent metal aluminum.
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31
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Breker M, Lieberman K, Cross FR. Comprehensive Discovery of Cell-Cycle-Essential Pathways in Chlamydomonas reinhardtii. THE PLANT CELL 2018; 30:1178-1198. [PMID: 29743196 PMCID: PMC6048789 DOI: 10.1105/tpc.18.00071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/26/2018] [Accepted: 05/08/2018] [Indexed: 05/05/2023]
Abstract
We generated a large collection of temperature-sensitive lethal mutants in the unicellular green alga Chlamydomonas reinhardtii, focusing on mutations specifically affecting cell cycle regulation. We used UV mutagenesis and robotically assisted phenotypic screening to isolate candidates. To overcome the bottleneck at the critical step of molecular identification of the causative mutation ("driver"), we developed MAPS-SEQ (meiosis-assisted purifying selection sequencing), a multiplexed genetic/bioinformatics strategy. MAPS-SEQ allowed us to perform multiplexed simultaneous determination of the driver mutations from hundreds of neutral "passenger" mutations in each member of a large pool of mutants. This method should work broadly, including in multicellular diploid genetic systems, for any scorable trait. Using MAPS-SEQ, we identified essential genes spanning a wide range of molecular functions. Phenotypic clustering based on DNA content analysis and cell morphology indicated that the mutated genes function in the cell cycle at multiple points and by diverse mechanisms. The collection is sufficiently complete to allow specific conditional inactivation of almost all cell-cycle-regulatory pathways. Approximately seventy-five percent of the essential genes identified in this project had clear orthologs in land plant genomes, a huge enrichment compared with the value of ∼20% for the Chlamydomonas genome overall. Findings about these mutants will likely have direct relevance to essential cell biology in land plants.
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Affiliation(s)
- Michal Breker
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, New York 10065
| | - Kristi Lieberman
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, New York 10065
| | - Frederick R Cross
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, New York 10065
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32
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Johnson RA, Conklin PA, Tjahjadi M, Missirian V, Toal T, Brady SM, Britt AB. SUPPRESSOR OF GAMMA RESPONSE1 Links DNA Damage Response to Organ Regeneration. PLANT PHYSIOLOGY 2018; 176:1665-1675. [PMID: 29222192 PMCID: PMC5813563 DOI: 10.1104/pp.17.01274] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/02/2017] [Indexed: 05/17/2023]
Abstract
In Arabidopsis, DNA damage-induced programmed cell death is limited to the meristematic stem cell niche and its early descendants. The significance of this cell-type-specific programmed cell death is unclear. Here, we demonstrate in roots that it is the programmed destruction of the mitotically compromised stem cell niche that triggers its regeneration, enabling growth recovery. In contrast to wild-type plants, sog1 plants, which are defective in damage-induced programmed cell death, maintain the cell identities and stereotypical structure of the stem cell niche after irradiation, but these cells fail to undergo cell division, terminating root growth. We propose DNA damage-induced programmed cell death is employed by plants as a developmental response, contrasting with its role as an anticarcinogenic response in animals. This role in plants may have evolved to restore the growth of embryos after the accumulation of DNA damage in seeds.
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Affiliation(s)
- Ross A Johnson
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
| | - Phillip A Conklin
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
| | - Michelle Tjahjadi
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
| | - Victor Missirian
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
| | - Ted Toal
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
| | - Siobhan M Brady
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
| | - Anne B Britt
- Department of Plant Biology, University of California Davis, 1 Shields Avenue, Davis, California 95616
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33
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Wei J, Zhang L, Ren L, Zhang J, Liu J, Duan J, Yu Y, Li Y, Peng C, Zhou X, Sun Z. Endosulfan induces cell dysfunction through cycle arrest resulting from DNA damage and DNA damage response signaling pathways. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 589:97-106. [PMID: 28273598 DOI: 10.1016/j.scitotenv.2017.02.154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 02/07/2017] [Accepted: 02/18/2017] [Indexed: 06/06/2023]
Abstract
Our previous study showed that endosulfan increases the risk of cardiovascular disease. To identify toxic mechanism of endosulfan, we conducted an animal study for which 32 male Wistar rats were randomly and equally divided into four groups: Control group (corn oil only) and three treatment groups (1, 5 and 10mgkg-1·d-1). The results showed that exposure to endosulfan resulted in injury of cardiac tissue with impaired mitochondria integrity and elevated 8-OHdG expression in myocardial cells. Moreover, endosulfan increased the expressions of Fas, FasL, Caspase-8, Cleaved Caspase-8, Caspase-3 and Cleaved Caspase-3 in cardiac tissue. In vitro, human umbilical vein endothelial cells (HUVECs) were treated with different concentrations of endosulfan (1, 6 and 12μgmL-1) for 24h. An inhibitor for Ataxia Telangiectasia Mutated Protein (ATM) (Ku-55933, 10μM) was added in 12μgmL-1 group for 2h before exposure to endosulfan. Results showed that endosulfan induced DNA damage and activated DNA damage response signaling pathway (ATM/Chk2 and ATR/Chk1) and consequent cell cycle checkpoint. Furthermore, endosulfan promoted the cell apoptosis through death receptor pathway resulting from oxidative stress. The results provide a new insight for mechanism of endosulfan-induced cardiovascular toxicity which will be helpful in future prevention of cardiovascular diseases induced by endosulfan.
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Affiliation(s)
- Jialiu Wei
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Lianshuang Zhang
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Lihua Ren
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Jin Zhang
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Jianhui Liu
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Junchao Duan
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Yang Yu
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Yanbo Li
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Cheng Peng
- National Research Centre for Environmental Toxicology (Entox), Queensland Alliance for Environmental Health Science (QAEHS), The University of Queensland, Coopers Plains, Brisbane, QLD 4108, Australia
| | - Xianqing Zhou
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China.
| | - Zhiwei Sun
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, 100069 Beijing, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
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Horvath BM, Kourova H, Nagy S, Nemeth E, Magyar Z, Papdi C, Ahmad Z, Sanchez-Perez GF, Perilli S, Blilou I, Pettkó-Szandtner A, Darula Z, Meszaros T, Binarova P, Bogre L, Scheres B. Arabidopsis RETINOBLASTOMA RELATED directly regulates DNA damage responses through functions beyond cell cycle control. EMBO J 2017; 36:1261-1278. [PMID: 28320736 PMCID: PMC5412863 DOI: 10.15252/embj.201694561] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 12/26/2022] Open
Abstract
The rapidly proliferating cells in plant meristems must be protected from genome damage. Here, we show that the regulatory role of the Arabidopsis RETINOBLASTOMA RELATED (RBR) in cell proliferation can be separated from a novel function in safeguarding genome integrity. Upon DNA damage, RBR and its binding partner E2FA are recruited to heterochromatic γH2AX-labelled DNA damage foci in an ATM- and ATR-dependent manner. These γH2AX-labelled DNA lesions are more dispersedly occupied by the conserved repair protein, AtBRCA1, which can also co-localise with RBR foci. RBR and AtBRCA1 physically interact in vitro and in planta Genetic interaction between the RBR-silenced amiRBR and Atbrca1 mutants suggests that RBR and AtBRCA1 may function together in maintaining genome integrity. Together with E2FA, RBR is directly involved in the transcriptional DNA damage response as well as in the cell death pathway that is independent of SOG1, the plant functional analogue of p53. Thus, plant homologs and analogues of major mammalian tumour suppressor proteins form a regulatory network that coordinates cell proliferation with cell and genome integrity.
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Affiliation(s)
- Beatrix M Horvath
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
| | - Hana Kourova
- Institute of Microbiology CAS, v.v.i., Laboratory of Cell Reproduction, Prague 4, Czech Republic
| | - Szilvia Nagy
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Edit Nemeth
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Zoltan Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Csaba Papdi
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Zaki Ahmad
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Gabino F Sanchez-Perez
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
| | - Serena Perilli
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
| | - Ikram Blilou
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
| | | | - Zsuzsanna Darula
- Laboratory of Proteomic Research, Biological Research Centre, Szeged, Hungary
| | - Tamas Meszaros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
- Technical Analytical Research Group of HAS, Budapest, Hungary
| | - Pavla Binarova
- Institute of Microbiology CAS, v.v.i., Laboratory of Cell Reproduction, Prague 4, Czech Republic
| | - Laszlo Bogre
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Ben Scheres
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
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35
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Biedermann S, Harashima H, Chen P, Heese M, Bouyer D, Sofroni K, Schnittger A. The retinoblastoma homolog RBR1 mediates localization of the repair protein RAD51 to DNA lesions in Arabidopsis. EMBO J 2017; 36:1279-1297. [PMID: 28320735 PMCID: PMC5412766 DOI: 10.15252/embj.201694571] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 02/17/2017] [Accepted: 02/20/2017] [Indexed: 11/13/2022] Open
Abstract
The retinoblastoma protein (Rb), which typically functions as a transcriptional repressor of E2F‐regulated genes, represents a major control hub of the cell cycle. Here, we show that loss of the Arabidopsis Rb homolog RETINOBLASTOMA‐RELATED 1 (RBR1) leads to cell death, especially upon exposure to genotoxic drugs such as the environmental toxin aluminum. While cell death can be suppressed by reduced cell‐proliferation rates, rbr1 mutant cells exhibit elevated levels of DNA lesions, indicating a direct role of RBR1 in the DNA‐damage response (DDR). Consistent with its role as a transcriptional repressor, we find that RBR1 directly binds to and represses key DDR genes such as RADIATION SENSITIVE 51 (RAD51), leaving it unclear why rbr1 mutants are hypersensitive to DNA damage. However, we find that RBR1 is also required for RAD51 localization to DNA lesions. We further show that RBR1 is itself targeted to DNA break sites in a CDKB1 activity‐dependent manner and partially co‐localizes with RAD51 at damage sites. Taken together, these results implicate RBR1 in the assembly of DNA‐bound repair complexes, in addition to its canonical function as a transcriptional regulator.
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Affiliation(s)
- Sascha Biedermann
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France.,Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
| | | | - Poyu Chen
- Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
| | - Maren Heese
- Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
| | - Daniel Bouyer
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197-INSERM U 1024, Paris, France
| | - Kostika Sofroni
- Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
| | - Arp Schnittger
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France .,Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
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36
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Pedroza-García JA, Mazubert C, Del Olmo I, Bourge M, Domenichini S, Bounon R, Tariq Z, Delannoy E, Piñeiro M, Jarillo JA, Bergounioux C, Benhamed M, Raynaud C. Function of the Plant DNA Polymerase Epsilon in Replicative Stress Sensing, a Genetic Analysis. PLANT PHYSIOLOGY 2017; 173:1735-1749. [PMID: 28153919 PMCID: PMC5338674 DOI: 10.1104/pp.17.00031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/30/2017] [Indexed: 05/17/2023]
Abstract
Faithful transmission of the genetic information is essential in all living organisms. DNA replication is therefore a critical step of cell proliferation, because of the potential occurrence of replication errors or DNA damage when progression of a replication fork is hampered causing replicative stress. Like other types of DNA damage, replicative stress activates the DNA damage response, a signaling cascade allowing cell cycle arrest and repair of lesions. The replicative DNA polymerase ε (Pol ε) was shown to activate the S-phase checkpoint in yeast in response to replicative stress, but whether this mechanism functions in multicellular eukaryotes remains unclear. Here, we explored the genetic interaction between Pol ε and the main elements of the DNA damage response in Arabidopsis (Arabidopsis thaliana). We found that mutations affecting the polymerase domain of Pol ε trigger ATR-dependent signaling leading to SOG1 activation, WEE1-dependent cell cycle inhibition, and tolerance to replicative stress induced by hydroxyurea, but result in enhanced sensitivity to a wide range of DNA damaging agents. Using knock-down lines, we also provide evidence for the direct role of Pol ε in replicative stress sensing. Together, our results demonstrate that the role of Pol ε in replicative stress sensing is conserved in plants, and provide, to our knowledge, the first genetic dissection of the downstream signaling events in a multicellular eukaryote.
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Affiliation(s)
- José-Antonio Pedroza-García
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Christelle Mazubert
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Ivan Del Olmo
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Mickael Bourge
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Séverine Domenichini
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Rémi Bounon
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Zakia Tariq
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Manuel Piñeiro
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - José A Jarillo
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.)
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.);
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France (J.A.P.-G., C.M., S.D., R.B., Z.T., E.D., C.B., M.B., C.R.);
- Centro de Biotecnología y Genómica de Plantas Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM 28223-Pozuelo de Alarcón (Madrid), Spain (I.d.O., M.P., J.A.J.); and
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France (M.B.)
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37
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Gutierrez C. 25 Years of Cell Cycle Research: What's Ahead? TRENDS IN PLANT SCIENCE 2016; 21:823-833. [PMID: 27401252 DOI: 10.1016/j.tplants.2016.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/13/2016] [Accepted: 06/21/2016] [Indexed: 05/27/2023]
Abstract
We have reached 25 years since the first molecular approaches to plant cell cycle. Fortunately, we have witnessed an enormous advance in this field that has benefited from using complementary approaches including molecular, cellular, genetic and genomic resources. These studies have also branched and demonstrated the functional relevance of cell cycle regulators for virtually every aspect of plant life. The question is - where are we heading? I review here the latest developments in the field and briefly elaborate on how new technological advances should contribute to novel approaches that will benefit the plant cell cycle field. Understanding how the cell division cycle is integrated at the organismal level is perhaps one of the major challenges.
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Affiliation(s)
- Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Nicolas Cabrera 1, 28049 Madrid, Spain.
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38
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DNA damage checkpoint kinase ATM regulates germination and maintains genome stability in seeds. Proc Natl Acad Sci U S A 2016; 113:9647-52. [PMID: 27503884 DOI: 10.1073/pnas.1608829113] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Genome integrity is crucial for cellular survival and the faithful transmission of genetic information. The eukaryotic cellular response to DNA damage is orchestrated by the DNA damage checkpoint kinases ATAXIA TELANGIECTASIA MUTATED (ATM) and ATM AND RAD3-RELATED (ATR). Here we identify important physiological roles for these sensor kinases in control of seed germination. We demonstrate that double-strand breaks (DSBs) are rate-limiting for germination. We identify that desiccation tolerant seeds exhibit a striking transcriptional DSB damage response during germination, indicative of high levels of genotoxic stress, which is induced following maturation drying and quiescence. Mutant atr and atm seeds are highly resistant to aging, establishing ATM and ATR as determinants of seed viability. In response to aging, ATM delays germination, whereas atm mutant seeds germinate with extensive chromosomal abnormalities. This identifies ATM as a major factor that controls germination in aged seeds, integrating progression through germination with surveillance of genome integrity. Mechanistically, ATM functions through control of DNA replication in imbibing seeds. ATM signaling is mediated by transcriptional control of the cell cycle inhibitor SIAMESE-RELATED 5, an essential factor required for the aging-induced delay to germination. In the soil seed bank, seeds exhibit increased transcript levels of ATM and ATR, with changes in dormancy and germination potential modulated by environmental signals, including temperature and soil moisture. Collectively, our findings reveal physiological functions for these sensor kinases in linking genome integrity to germination, thereby influencing seed quality, crucial for plant survival in the natural environment and sustainable crop production.
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Weimer AK, Biedermann S, Harashima H, Roodbarkelari F, Takahashi N, Foreman J, Guan Y, Pochon G, Heese M, Van Damme D, Sugimoto K, Koncz C, Doerner P, Umeda M, Schnittger A. The plant-specific CDKB1-CYCB1 complex mediates homologous recombination repair in Arabidopsis. EMBO J 2016; 35:2068-2086. [PMID: 27497297 PMCID: PMC5048351 DOI: 10.15252/embj.201593083] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 07/14/2016] [Indexed: 01/30/2023] Open
Abstract
Upon DNA damage, cyclin‐dependent kinases (CDKs) are typically inhibited to block cell division. In many organisms, however, it has been found that CDK activity is required for DNA repair, especially for homology‐dependent repair (HR), resulting in the conundrum how mitotic arrest and repair can be reconciled. Here, we show that Arabidopsis thaliana solves this dilemma by a division of labor strategy. We identify the plant‐specific B1‐type CDKs (CDKB1s) and the class of B1‐type cyclins (CYCB1s) as major regulators of HR in plants. We find that RADIATION SENSITIVE 51 (RAD51), a core mediator of HR, is a substrate of CDKB1‐CYCB1 complexes. Conversely, mutants in CDKB1 and CYCB1 fail to recruit RAD51 to damaged DNA. CYCB1;1 is specifically activated after DNA damage and we show that this activation is directly controlled by SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a transcription factor that acts similarly to p53 in animals. Thus, while the major mitotic cell‐cycle activity is blocked after DNA damage, CDKB1‐CYCB1 complexes are specifically activated to mediate HR.
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Affiliation(s)
- Annika K Weimer
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Sascha Biedermann
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | | | | | - Naoki Takahashi
- Plant Growth Regulation Laboratory, Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara, Japan
| | - Julia Foreman
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Yonsheng Guan
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Gaëtan Pochon
- Department of Developmental Biology, Biozentrum Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Maren Heese
- Department of Developmental Biology, Biozentrum Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Daniël Van Damme
- Department of Plant Systems Biology, VIB, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Japan
| | - Csaba Koncz
- Max-Planck-Institut für Pflanzenzüchtungsforschung, Köln, Germany
| | - Peter Doerner
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Masaaki Umeda
- Plant Growth Regulation Laboratory, Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara, Japan JST, CREST, Ikoma, Nara, Japan
| | - Arp Schnittger
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS UPR2357, Université de Strasbourg, Strasbourg Cedex, France Department of Developmental Biology, Biozentrum Klein Flottbek, University of Hamburg, Hamburg, Germany Trinationales Institut für Pflanzenforschung, Institut de Biologie Moléculaire des Plantes du CNRS, IBMP-CNRS, Strasbourg Cedex, France
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40
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Abstract
Because the genome stores all genetic information required for growth and development, it is of pivotal importance to maintain DNA integrity, especially during cell division, when the genome is prone to replication errors and damage. Although over the last two decades it has become evident that the basic cell cycle toolbox of plants shares several similarities with those of fungi and mammals, plants appear to have evolved a set of distinct checkpoint regulators in response to different types of DNA stress. This might be a consequence of plants' sessile lifestyle, which exposes them to a set of unique DNA damage-inducing conditions. In this review, we highlight the types of DNA stress that plants typically experience and describe the plant-specific molecular mechanisms that control cell division in response to these stresses.
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Affiliation(s)
- Zhubing Hu
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
| | - Toon Cools
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium
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Slovak R, Ogura T, Satbhai SB, Ristova D, Busch W. Genetic control of root growth: from genes to networks. ANNALS OF BOTANY 2016; 117:9-24. [PMID: 26558398 PMCID: PMC4701154 DOI: 10.1093/aob/mcv160] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/28/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Roots are essential organs for higher plants. They provide the plant with nutrients and water, anchor the plant in the soil, and can serve as energy storage organs. One remarkable feature of roots is that they are able to adjust their growth to changing environments. This adjustment is possible through mechanisms that modulate a diverse set of root traits such as growth rate, diameter, growth direction and lateral root formation. The basis of these traits and their modulation are at the cellular level, where a multitude of genes and gene networks precisely regulate development in time and space and tune it to environmental conditions. SCOPE This review first describes the root system and then presents fundamental work that has shed light on the basic regulatory principles of root growth and development. It then considers emerging complexities and how they have been addressed using systems-biology approaches, and then describes and argues for a systems-genetics approach. For reasons of simplicity and conciseness, this review is mostly limited to work from the model plant Arabidopsis thaliana, in which much of the research in root growth regulation at the molecular level has been conducted. CONCLUSIONS While forward genetic approaches have identified key regulators and genetic pathways, systems-biology approaches have been successful in shedding light on complex biological processes, for instance molecular mechanisms involving the quantitative interaction of several molecular components, or the interaction of large numbers of genes. However, there are significant limitations in many of these methods for capturing dynamic processes, as well as relating these processes to genotypic and phenotypic variation. The emerging field of systems genetics promises to overcome some of these limitations by linking genotypes to complex phenotypic and molecular data using approaches from different fields, such as genetics, genomics, systems biology and phenomics.
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Affiliation(s)
- Radka Slovak
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Takehiko Ogura
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Santosh B Satbhai
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Daniela Ristova
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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42
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Zhang Y, Wen C, Liu S, Zheng L, Shen B, Tao Y. Shade avoidance 6 encodes an Arabidopsis flap endonuclease required for maintenance of genome integrity and development. Nucleic Acids Res 2015; 44:1271-84. [PMID: 26721386 PMCID: PMC4756833 DOI: 10.1093/nar/gkv1474] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 12/03/2015] [Indexed: 12/01/2022] Open
Abstract
Flap endonuclease-1 (FEN1) belongs to the Rad2 family of structure-specific nucleases. It is required for several DNA metabolic pathways, including DNA replication and DNA damage repair. Here, we have identified a shade avoidance mutant, sav6, which reduces the mRNA splicing efficiency of SAV6. We have demonstrated that SAV6 is an FEN1 homologue that shows double-flap endonuclease and gap-dependent endonuclease activity, but lacks exonuclease activity. sav6 mutants are hypersensitive to DNA damage induced by ultraviolet (UV)-C radiation and reagents that induce double-stranded DNA breaks, but exhibit normal responses to chemicals that block DNA replication. Signalling components that respond to DNA damage are constitutively activated in sav6 mutants. These data indicate that SAV6 is required for DNA damage repair and the maintenance of genome integrity. Mutant sav6 plants also show reduced root apical meristem (RAM) size and defective quiescent centre (QC) development. The expression of SMR7, a cell cycle regulatory gene, and ERF115 and PSK5, regulators of QC division, is increased in sav6 mutants. Their constitutive induction is likely due to the elevated DNA damage responses in sav6 and may lead to defects in the development of the RAM and QC. Therefore, SAV6 assures proper root development through maintenance of genome integrity.
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Affiliation(s)
- Yijuan Zhang
- School of Life Sciences, Xiamen Plant Genetics Key Laboratory, Xiamen University, Xiamen 361102, China State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen 361102, China
| | - Chunhong Wen
- School of Life Sciences, Xiamen Plant Genetics Key Laboratory, Xiamen University, Xiamen 361102, China
| | - Songbai Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA College of Life Sciences, Zhejiang University, Hangzhou, China Suzhou Health College, Suzhou Key Laboratory of Biotechnology for Laboratory Medicine, Suzhou, 215009, Jiangsu Province, China
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Yi Tao
- School of Life Sciences, Xiamen Plant Genetics Key Laboratory, Xiamen University, Xiamen 361102, China State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen 361102, China
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Furukawa T, Angelis KJ, Britt AB. Arabidopsis DNA polymerase lambda mutant is mildly sensitive to DNA double strand breaks but defective in integration of a transgene. FRONTIERS IN PLANT SCIENCE 2015; 6:357. [PMID: 26074930 PMCID: PMC4444747 DOI: 10.3389/fpls.2015.00357] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 05/05/2015] [Indexed: 05/20/2023]
Abstract
The DNA double-strand break (DSB) is a critical type of damage, and can be induced by both endogenous sources (e.g., errors of oxidative metabolism, transposable elements, programmed meiotic breaks, or perturbation of the DNA replication fork) and exogenous sources (e.g., ionizing radiation or radiomimetic chemicals). Although higher plants, like mammals, are thought to preferentially repair DSBs via nonhomologous end joining (NHEJ), much remains unclear about plant DSB repair pathways. Our reverse genetic approach suggests that DNA polymerase λ is involved in DSB repair in Arabidopsis. The Arabidopsis T-DNA insertion mutant (atpolλ-1) displayed sensitivity to both gamma-irradiation and treatment with radiomimetic reagents, but not to other DNA damaging treatments. The atpolλ-1 mutant showed a moderate sensitivity to DSBs, while Arabidopsis Ku70 and DNA ligase 4 mutants (atku70-3 and atlig4-2), both of which play critical roles in NHEJ, exhibited a hypersensitivity to these treatments. The atpolλ-1/atlig4-2 double mutant exhibited a higher sensitivity to DSBs than each single mutant, but the atku70/atpolλ-1 showed similar sensitivity to the atku70-3 mutant. We showed that transcription of the DNA ligase 1, DNA ligase 6, and Wee1 genes was quickly induced by BLM in several NHEJ deficient mutants in contrast to wild-type. Finally, the T-DNA transformation efficiency dropped in NHEJ deficient mutants and the lowest transformation efficiency was scored in the atpolλ-1/atlig4-2 double mutant. These results imply that AtPolλ is involved in both DSB repair and DNA damage response pathway.
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Affiliation(s)
- Tomoyuki Furukawa
- Department of Plant Biology, University of California at DavisDavis, CA, USA
| | - Karel J. Angelis
- DNA Repair Lab, Institute of Experimental Botany of the Academy of Sciences of the Czech RepublicPraha, Czech Republic
| | - Anne B. Britt
- Department of Plant Biology, University of California at DavisDavis, CA, USA
- *Correspondence: Anne B. Britt, Department of Plant Biology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
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44
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Hu Z, Cools T, Kalhorzadeh P, Heyman J, De Veylder L. Deficiency of the Arabidopsis helicase RTEL1 triggers a SOG1-dependent replication checkpoint in response to DNA cross-links. THE PLANT CELL 2015; 27:149-61. [PMID: 25595823 PMCID: PMC4330584 DOI: 10.1105/tpc.114.134312] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
To maintain genome integrity, DNA replication is executed and regulated by a complex molecular network of numerous proteins, including helicases and cell cycle checkpoint regulators. Through a systematic screening for putative replication mutants, we identified an Arabidopsis thaliana homolog of human Regulator of Telomere Length 1 (RTEL1), which functions in DNA replication, DNA repair, and recombination. RTEL1 deficiency retards plant growth, a phenotype including a prolonged S-phase duration and decreased cell proliferation. Genetic analysis revealed that rtel1 mutant plants show activated cell cycle checkpoints, specific sensitivity to DNA cross-linking agents, and increased homologous recombination, but a lack of progressive shortening of telomeres, indicating that RTEL1 functions have only been partially conserved between mammals and plants. Surprisingly, RTEL1 deficiency induces tolerance to the deoxynucleotide-depleting drug hydroxyurea, which could be mimicked by DNA cross-linking agents. This resistance does not rely on the essential replication checkpoint regulator WEE1 but could be blocked by a mutation in the SOG1 transcription factor. Taken together, our data indicate that RTEL1 is required for DNA replication and that its deficiency activates a SOG1-dependent replication checkpoint.
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Affiliation(s)
- Zhubing Hu
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Toon Cools
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Pooneh Kalhorzadeh
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Jefri Heyman
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Lieven De Veylder
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
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45
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Eekhout T, Kalhorzadeh P, De Veylder L. Lack of RNase H2 activity rescues HU-sensitivity of WEE1 deficient plants. PLANT SIGNALING & BEHAVIOR 2015; 10:e1001226. [PMID: 25875879 PMCID: PMC4622661 DOI: 10.1080/15592324.2014.1001226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Because of their sessile lifestyle, plants have developed extensive mechanisms to safeguard their genetic information from one generation to the next. The WEE1 kinase is one of the guardians of genome integrity, being important during S-phase progression under replication stress. Knock-out plants for WEE1 (WEE1(KO)) show a hypersensitive response when grown on replication-inhibiting drugs. Recently, we reported the identification of a mutant in the RNase H2A gene that could partially complement this replication phenotype. Here, we present the identification of a second member of the RNase H2 complex, RNase H2B, being able to complement the root growth phenotype of WEE1(KO) plants. We additionally show that deletion of a conserved domain in RNase H2B leads to loss of interaction with the RNase H2C subunit, likely explaining the loss of activity of the RNase H2 complex.
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Affiliation(s)
- Thomas Eekhout
- Department of Plant Systems Biology; Flanders Institute for Biotechnology (VIB); Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Ghent, Belgium
| | - Pooneh Kalhorzadeh
- Department of Plant Systems Biology; Flanders Institute for Biotechnology (VIB); Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Systems Biology; Flanders Institute for Biotechnology (VIB); Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Ghent, Belgium
- Correspondence to: Lieven De Veylder;
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46
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Kalhorzadeh P, Hu Z, Cools T, Amiard S, Willing EM, De Winne N, Gevaert K, De Jaeger G, Schneeberger K, White CI, De Veylder L. Arabidopsis thaliana RNase H2 deficiency counteracts the needs for the WEE1 checkpoint kinase but triggers genome instability. THE PLANT CELL 2014; 26:3680-92. [PMID: 25217508 PMCID: PMC4213155 DOI: 10.1105/tpc.114.128108] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The WEE1 kinase is an essential cell cycle checkpoint regulator in Arabidopsis thaliana plants experiencing replication defects. Whereas under non-stress conditions WEE1-deficient plants develop normally, they fail to adapt to replication inhibitory conditions, resulting in the accumulation of DNA damage and loss of cell division competence. We identified mutant alleles of the genes encoding subunits of the ribonuclease H2 (RNase H2) complex, known for its role in removing ribonucleotides from DNA-RNA duplexes, as suppressor mutants of WEE1 knockout plants. RNase H2 deficiency triggered an increase in homologous recombination (HR), correlated with the accumulation of γ-H2AX foci. However, as HR negatively impacts the growth of WEE1-deficient plants under replication stress, it cannot account for the rescue of the replication defects of the WEE1 knockout plants. Rather, the observed increase in ribonucleotide incorporation in DNA indicates that the substitution of deoxynucleotide with ribonucleotide abolishes the need for WEE1 under replication stress. Strikingly, increased ribonucleotide incorporation in DNA correlated with the occurrence of small base pair deletions, identifying the RNase H2 complex as an important suppressor of genome instability.
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Affiliation(s)
- Pooneh Kalhorzadeh
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Zhubing Hu
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Toon Cools
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Simon Amiard
- Génétique, Reproduction et Développement, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 6293-Clermont Université-Institut National de la Santé et de la Recherche Médicale U1103, F-63177 Aubière, France
| | - Eva-Maria Willing
- Department for Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Nancy De Winne
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, Flanders Institute for Biotechnology (VIB), B-9000 Ghent, Belgium Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Korbinian Schneeberger
- Department for Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Charles I White
- Génétique, Reproduction et Développement, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 6293-Clermont Université-Institut National de la Santé et de la Recherche Médicale U1103, F-63177 Aubière, France
| | - Lieven De Veylder
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
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47
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Missirian V, Conklin PA, Culligan KM, Huefner ND, Britt AB. High atomic weight, high-energy radiation (HZE) induces transcriptional responses shared with conventional stresses in addition to a core "DSB" response specific to clastogenic treatments. FRONTIERS IN PLANT SCIENCE 2014; 5:364. [PMID: 25136344 PMCID: PMC4117989 DOI: 10.3389/fpls.2014.00364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 07/08/2014] [Indexed: 05/19/2023]
Abstract
Plants exhibit a robust transcriptional response to gamma radiation which includes the induction of transcripts required for homologous recombination and the suppression of transcripts that promote cell cycle progression. Various DNA damaging agents induce different spectra of DNA damage as well as "collateral" damage to other cellular components and therefore are not expected to provoke identical responses by the cell. Here we study the effects of two different types of ionizing radiation (IR) treatment, HZE (1 GeV Fe(26+) high mass, high charge, and high energy relativistic particles) and gamma photons, on the transcriptome of Arabidopsis thaliana seedlings. Both types of IR induce small clusters of radicals that can result in the formation of double strand breaks (DSBs), but HZE also produces linear arrays of extremely clustered damage. We performed these experiments across a range of time points (1.5-24 h after irradiation) in both wild-type plants and in mutants defective in the DSB-sensing protein kinase ATM. The two types of IR exhibit a shared double strand break-repair-related damage response, although they differ slightly in the timing, degree, and ATM-dependence of the response. The ATM-dependent, DNA metabolism-related transcripts of the "DSB response" were also induced by other DNA damaging agents, but were not induced by conventional stresses. Both Gamma and HZE irradiation induced, at 24 h post-irradiation, ATM-dependent transcripts associated with a variety of conventional stresses; these were overrepresented for pathogen response, rather than DNA metabolism. In contrast, only HZE-irradiated plants, at 1.5 h after irradiation, exhibited an additional and very extensive transcriptional response, shared with plants experiencing "extended night." This response was not apparent in gamma-irradiated plants.
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Affiliation(s)
- Victor Missirian
- Department of Plant Biology, University of California DavisDavis, CA, USA
| | - Phillip A. Conklin
- Department of Plant Biology, University of California DavisDavis, CA, USA
| | - Kevin M. Culligan
- Department of Molecular, Cellular, and Biomedical Sciences, University of New HampshireDurham, NH, USA
| | - Neil D. Huefner
- Department of Plant Biology, University of California DavisDavis, CA, USA
| | - Anne B. Britt
- Department of Plant Biology, University of California DavisDavis, CA, USA
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48
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Chevalier C, Bourdon M, Pirrello J, Cheniclet C, Gévaudant F, Frangne N. Endoreduplication and fruit growth in tomato: evidence in favour of the karyoplasmic ratio theory. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2731-46. [PMID: 24187421 DOI: 10.1093/jxb/ert366] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The growth of a plant organ depends upon the developmental processes of cell division and cell expansion. The activity of cell divisions sets the number of cells that will make up the organ; the cell expansion activity then determines its final size. Among the various mechanisms that may influence the determination of cell size, endopolyploidy by means of endoreduplication appears to be of great importance in plants. Endoreduplication is widespread in plants and supports the process of differentiation of cells and organs. Its functional role in plant cells is not fully understood, although it is commonly associated with ploidy-dependent cell expansion. During the development of tomato fruit, cells from the (fleshy) pericarp tissue become highly polyploid, reaching a DNA content barely encountered in other plant species (between 2C and 512C). Recent investigations using tomato fruit development as a model provided new data in favour of the long-standing karyoplasmic ratio theory, stating that cells tend to adjust their cytoplasmic volume to the nuclear DNA content. By establishing a highly structured cellular system where multiple physiological functions are integrated, endoreduplication does act as a morphogenetic factor supporting cell growth during tomato fruit development.
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Affiliation(s)
- Christian Chevalier
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
| | - Matthieu Bourdon
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
| | - Julien Pirrello
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
| | - Catherine Cheniclet
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France CNRS, Bordeaux Imaging Center, UMS 3420, F-33000 Bordeaux, France
| | - Frédéric Gévaudant
- University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
| | - Nathalie Frangne
- University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
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49
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Pecinka A, Liu CH. Drugs for Plant Chromosome and Chromatin Research. Cytogenet Genome Res 2014; 143:51-9. [DOI: 10.1159/000360774] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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50
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Juraniec M, Lequeux H, Hermans C, Willems G, Nordborg M, Schneeberger K, Salis P, Vromant M, Lutts S, Verbruggen N. Towards the discovery of novel genetic component involved in stress resistance in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2014; 201:810-824. [PMID: 24134393 DOI: 10.1111/nph.12554] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/16/2013] [Indexed: 05/23/2023]
Abstract
The exposure of plants to high concentrations of trace metallic elements such as copper involves a remodeling of the root system, characterized by a primary root growth inhibition and an increase in the lateral root density. These characteristics constitute easy and suitable markers for screening mutants altered in their response to copper excess. A forward genetic approach was undertaken in order to discover novel genetic factors involved in the response to copper excess. A Cu(2+) -sensitive mutant named copper modified resistance1 (cmr1) was isolated and a causative mutation in the CMR1 gene was identified by using positional cloning and next-generation sequencing. CMR1 encodes a plant-specific protein of unknown function. The analysis of the cmr1 mutant indicates that the CMR1 protein is required for optimal growth under normal conditions and has an essential role in the stress response. Impairment of the CMR1 activity alters root growth through aberrant activity of the root meristem, and modifies potassium concentration and hormonal balance (ethylene production and auxin accumulation). Our data support a putative role for CMR1 in cell division regulation and meristem maintenance. Research on the role of CMR1 will contribute to the understanding of the plasticity of plants in response to changing environments.
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Affiliation(s)
- Michal Juraniec
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Hélène Lequeux
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université catholique de Louvain, 5 bte13, Croix du Sud, 1348, Louvain-La-Neuve, Belgium
| | - Christian Hermans
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Glenda Willems
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Korbinian Schneeberger
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Pietrino Salis
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Maud Vromant
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Stanley Lutts
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université catholique de Louvain, 5 bte13, Croix du Sud, 1348, Louvain-La-Neuve, Belgium
| | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
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