1
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Fan L, Wei Y, Chen Y, Ouaziz M, Jiang S, Xu F, Wang H, Shao X. Transcriptome analysis reveals the mechanism of antifungal peptide epinecidin-1 against Botrytis cinerea by mitochondrial dysfunction and oxidative stress. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 202:105932. [PMID: 38879298 DOI: 10.1016/j.pestbp.2024.105932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/20/2024] [Accepted: 04/26/2024] [Indexed: 06/19/2024]
Abstract
The marine antifungal peptide epinecidin-1 (EPI) have been shown to inhibit Botrytis cinerea growth, while the molecular mechanism have not been explored based on omics technology. This study aimed to investigate the molecular mechanism of EPI against B. cinerea by transcriptome technology. Our findings indicated that a total of 1671 differentially expressed genes (DEGs) were detected in the mycelium of B. cinerea treated with 12.5 μmol/L EPI for 3 h, including 773 up-regulated genes and 898 down-regulated genes. Cluster analysis showed that DEGs (including steroid biosynthesis, (unsaturated) fatty acid biosynthesis) related to cell membrane metabolism were significantly down-regulated, and almost all DEGs involved in DNA replication were significantly inhibited. In addition, it also induced the activation of stress-related pathways, such as the antioxidant system, ATP-binding cassette transporter (ABC) and MAPK signaling pathways, and interfered with the tricarboxylic acid (TCA) cycle and oxidative phosphorylation pathways related to mitochondrial function. The decrease of mitochondrial related enzyme activities (succinate dehydrogenase, malate dehydrogenase and adenosine triphosphatase), the decrease of mitochondrial membrane potential and the increase content of hydrogen peroxide further confirmed that EPI treatment may lead to mitochondrial dysfunction and oxidative stress. Based on this, we speculated that EPI may impede the growth of B. cinerea through its influence on gene expression, and may lead to mitochondrial dysfunction and oxidative stress.
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Affiliation(s)
- Li Fan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food Science and Engineering, Ningbo University, Ningbo 315800, China; College of Biological Environment, JiYang College of Zhejiang A&F University, Zhuji 311800, China
| | - Yingying Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food Science and Engineering, Ningbo University, Ningbo 315800, China
| | - Yi Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food Science and Engineering, Ningbo University, Ningbo 315800, China
| | - Meriem Ouaziz
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food Science and Engineering, Ningbo University, Ningbo 315800, China
| | - Shu Jiang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food Science and Engineering, Ningbo University, Ningbo 315800, China
| | - Feng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food Science and Engineering, Ningbo University, Ningbo 315800, China
| | - Hongfei Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food Science and Engineering, Ningbo University, Ningbo 315800, China
| | - Xingfeng Shao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food Science and Engineering, Ningbo University, Ningbo 315800, China.
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2
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Li Q, Zhou J, Li S, Zhang W, Du Y, Li K, Wang Y, Sun Q. DNA polymerase ε harmonizes topological states and R-loops formation to maintain genome integrity in Arabidopsis. Nat Commun 2023; 14:7763. [PMID: 38012183 PMCID: PMC10682485 DOI: 10.1038/s41467-023-43680-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/16/2023] [Indexed: 11/29/2023] Open
Abstract
Genome topology is tied to R-loop formation and genome stability. However, the regulatory mechanism remains to be elucidated. By establishing a system to sense the connections between R-loops and genome topology states, we show that inhibiting DNA topoisomerase 1 (TOP1i) triggers the global increase of R-loops (called topoR-loops) and DNA damages, which are exacerbated in the DNA damage repair-compromised mutant atm. A suppressor screen identifies a mutation in POL2A, the catalytic subunit of DNA polymerase ε, rescuing the TOP1i-induced topoR-loop accumulation and genome instability in atm. Importantly we find that a highly conserved junction domain between the exonuclease and polymerase domains in POL2A is required for modulating topoR-loops near DNA replication origins and facilitating faithful DNA replication. Our results suggest that DNA replication acts in concert with genome topological states to fine-tune R-loops and thereby maintain genome integrity, revealing a likely conserved regulatory mechanism of TOP1i resistance in chemotherapy for ATM-deficient cancers.
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Affiliation(s)
- Qin Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jincong Zhou
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Shuai Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yingxue Du
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Yingxiang Wang
- College of Life Science, South China Agricultural University, Guangdong Laboratory for Lingnan Morden Agriculture, Guangzhou, 510642, China
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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3
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Nisa M, Eekhout T, Bergis C, Pedroza-Garcia JA, He X, Mazubert C, Vercauteren I, Cools T, Brik-Chaouche R, Drouin-Wahbi J, Chmaiss L, Latrasse D, Bergounioux C, Vandepoele K, Benhamed M, De Veylder L, Raynaud C. Distinctive and complementary roles of E2F transcription factors during plant replication stress responses. MOLECULAR PLANT 2023; 16:1269-1282. [PMID: 37415334 DOI: 10.1016/j.molp.2023.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/22/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Survival of living organisms is fully dependent on their maintenance of genome integrity, being permanently threatened by replication stress in proliferating cells. Although the plant DNA damage response (DDR) regulator SOG1 has been demonstrated to cope with replication defects, accumulating evidence points to other pathways functioning independent of SOG1. Here, we report the roles of the Arabidopsis E2FA and EF2B transcription factors, two well-characterized regulators of DNA replication, in plant response to replication stress. Through a combination of reverse genetics and chromatin immunoprecipitation approaches, we show that E2FA and E2FB share many target genes with SOG1, providing evidence for their involvement in the DDR. Analysis of double- and triple-mutant combinations revealed that E2FB, rather than E2FA, plays the most prominent role in sustaining plant growth in the presence of replication defects, either operating antagonistically or synergistically with SOG1. Conversely, SOG1 aids in overcoming the replication defects of E2FA/E2FB-deficient plants. Collectively, our data reveal a complex transcriptional network controlling the replication stress response in which E2Fs and SOG1 act as key regulatory factors.
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Affiliation(s)
- Maherun Nisa
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Clara Bergis
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Jose-Antonio Pedroza-Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Xiaoning He
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Christelle Mazubert
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Toon Cools
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Rim Brik-Chaouche
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Jeannine Drouin-Wahbi
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Layla Chmaiss
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France.
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4
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Li J, Qian W. Translational control of SOG1 expression in response to replication stress in Arabidopsis. STRESS BIOLOGY 2023; 3:28. [PMID: 37676617 PMCID: PMC10442038 DOI: 10.1007/s44154-023-00112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023]
Abstract
DNA damage, which may arise from cellular activities or be induced by genotoxic stresses, can cause genome instability and significantly affect plant growth and productivity. In response to genotoxic stresses, plants activate the cellular DNA damage response (DDR) to sense the stresses and activate downstream processes. The transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a functional counterpart of mammalian p53, is a master regulator of the DDR in plants. It is activated by various types of DNA lesions and can activate the transcription of hundreds of genes to trigger downstream processes, including cell cycle arrest, DNA repair, endoreplication, and apoptosis. Since SOG1 plays a crucial role in DDR, the activity of SOG1 must be tightly regulated. A recent study published in Plant Cell (Chen et al., Plant Cell koad126, 2023) reports a novel mechanism by which the ATR-WEE1 kinase module promotes SOG1 translation to fine-tune replication stress response.
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Affiliation(s)
- Jinchao Li
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
| | - Weiqiang Qian
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
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5
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Li J, Wang C, Liang W, Zhang J, Jiang CK, Liu Y, Ren Z, Ci D, Chang J, Han S, Deng XW, Wang Y, Qian W. Functional importance and divergence of plant apurinic/apyrimidinic endonucleases in somatic and meiotic DNA repair. THE PLANT CELL 2023; 35:2316-2331. [PMID: 36856605 PMCID: PMC10226563 DOI: 10.1093/plcell/koad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 05/30/2023]
Abstract
Apurinic/apyrimidinic (AP) sites are one of the most abundant DNA lesions and are mainly repaired by AP endonucleases (APEs). While most eukaryotic genomes encode two APEs, plants usually possess three APEs, namely APE1L, APE2, and ARP. To date, the biological relevance and functional divergence of plant APEs are unclear. Here, we show that the three plant APEs have ancient origins, with the APE1L clade being plant-specific. In Arabidopsis thaliana, simultaneously mutating APE1L and APE2, but not ARP alone or in combination with either APE1L or APE2, results in clear developmental defects linked to genotoxic stress. Genetic analyses indicated that the three plant APEs have different substrate preferences in vivo. ARP is mainly responsible for AP site repair, while APE1L and APE2 prefer to repair 3'-blocked single-stranded DNA breaks. We further determined that APEs play an important role in DNA repair and the maintenance of genomic integrity in meiotic cells. The ape1l ape2 double mutant exhibited a greatly enhanced frequency of sporulation 1 (SPO11-1)-dependent and SPO11-1-independent double-stranded DNA breaks. The DNA damage response (DDR) was activated in ape1l ape2 to trigger pollen abortion. Our findings suggest functional divergence of plant APEs and reveal important roles of plant APEs during vegetative and reproductive development.
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Affiliation(s)
- Jinchao Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Cong Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Wenjie Liang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Jun Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chen-Kun Jiang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Yi Liu
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhitong Ren
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Dong Ci
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Shandong 261000, China
| | - Jinjie Chang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Shangling Han
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Shandong 261000, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Shandong 261000, China
| | - Yingxiang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Shandong 261000, China
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6
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Gutierrez C. A Journey to the Core of the Plant Cell Cycle. Int J Mol Sci 2022; 23:8154. [PMID: 35897730 PMCID: PMC9330084 DOI: 10.3390/ijms23158154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/16/2022] [Accepted: 07/21/2022] [Indexed: 02/04/2023] Open
Abstract
Production of new cells as a result of progression through the cell division cycle is a fundamental biological process for the perpetuation of both unicellular and multicellular organisms. In the case of plants, their developmental strategies and their largely sessile nature has imposed a series of evolutionary trends. Studies of the plant cell division cycle began with cytological and physiological approaches in the 1950s and 1960s. The decade of 1990 marked a turn point with the increasing development of novel cellular and molecular protocols combined with advances in genetics and, later, genomics, leading to an exponential growth of the field. In this article, I review the current status of plant cell cycle studies but also discuss early studies and the relevance of a multidisciplinary background as a source of innovative questions and answers. In addition to advances in a deeper understanding of the plant cell cycle machinery, current studies focus on the intimate interaction of cell cycle components with almost every aspect of plant biology.
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Affiliation(s)
- Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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7
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Wang M, Ogé L, Pérez Garcia MD, Launay-Avon A, Clément G, Le Gourrierec J, Hamama L, Sakr S. Antagonistic Effect of Sucrose Availability and Auxin on Rosa Axillary Bud Metabolism and Signaling, Based on the Transcriptomics and Metabolomics Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:830840. [PMID: 35392520 PMCID: PMC8982072 DOI: 10.3389/fpls.2022.830840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Shoot branching is crucial for successful plant development and plant response to environmental factors. Extensive investigations have revealed the involvement of an intricate regulatory network including hormones and sugars. Recent studies have demonstrated that two major systemic regulators-auxin and sugar-antagonistically regulate plant branching. However, little is known regarding the molecular mechanisms involved in this crosstalk. We carried out two complementary untargeted approaches-RNA-seq and metabolomics-on explant stem buds fed with different concentrations of auxin and sucrose resulting in dormant and non-dormant buds. Buds responded to the combined effect of auxin and sugar by massive reprogramming of the transcriptome and metabolome. The antagonistic effect of sucrose and auxin targeted several important physiological processes, including sink strength, the amino acid metabolism, the sulfate metabolism, ribosome biogenesis, the nucleic acid metabolism, and phytohormone signaling. Further experiments revealed a role of the TOR-kinase signaling pathway in bud outgrowth through at least downregulation of Rosa hybrida BRANCHED1 (RhBRC1). These new findings represent a cornerstone to further investigate the diverse molecular mechanisms that drive the integration of endogenous factors during shoot branching.
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Affiliation(s)
- Ming Wang
- Dryland-Technology Key Laboratory of Shandong Province, College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Institut Agro, University of Angers INRAE, IRHS, SFR QUASAV, Angers, France
| | - Laurent Ogé
- Institut Agro, University of Angers INRAE, IRHS, SFR QUASAV, Angers, France
| | | | - Alexandra Launay-Avon
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Gilles Clément
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Jose Le Gourrierec
- Institut Agro, University of Angers INRAE, IRHS, SFR QUASAV, Angers, France
| | - Latifa Hamama
- Institut Agro, University of Angers INRAE, IRHS, SFR QUASAV, Angers, France
| | - Soulaiman Sakr
- Institut Agro, University of Angers INRAE, IRHS, SFR QUASAV, Angers, France
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8
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Li J, Liang W, Liu Y, Ren Z, Ci D, Chang J, Qian W. The Arabidopsis ATR-SOG1 signaling module regulates pleiotropic developmental adjustments in response to 3'-blocked DNA repair intermediates. THE PLANT CELL 2022; 34:852-866. [PMID: 34791445 PMCID: PMC8824664 DOI: 10.1093/plcell/koab282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/08/2021] [Indexed: 06/01/2023]
Abstract
Base excision repair and active DNA demethylation produce repair intermediates with DNA molecules blocked at the 3'-OH end by an aldehyde or phosphate group. However, both the physiological consequences of these accumulated single-strand DNAs break with 3'-blocked ends (DNA 3'-blocks) and the signaling pathways responding to unrepaired DNA 3'-blocks remain unclear in plants. Here, we investigated the effects of DNA 3'-blocks on plant development using the zinc finger DNA 3'-phosphoesterase (zdp) AP endonuclease2 (ape2) double mutant, in which 3'-blocking residues are poorly repaired. The accumulation of DNA 3'-blocked triggered diverse developmental defects that were dependent on the ATM and RAD3-related (ATR)-suppressor of gamma response 1 (SOG1) signaling module. SOG1 mutation rescued the developmental defects of zdp ape2 leaves by preventing cell endoreplication and promoting cell proliferation. However, SOG1 mutation caused intensive meristematic cell death in the radicle of zdp ape2 following germination, resulting in rapid termination of radicle growth. Notably, mutating FORMAMIDOPYRIMIDINE DNA GLYCOSYLASE (FPG) in zdp ape2 sog1 partially recovered its radicle growth, demonstrating that DNA 3'-blocks generated by FPG caused the meristematic defects. Surprisingly, despite lacking a functional radicle, zdp ape2 sog1 mutants compensated the lack of root growth by generating anchor roots having low levels of DNA damage response. Our results reveal dual roles of SOG1 in regulating root establishment when seeds germinate with excess DNA 3'-blocks.
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Affiliation(s)
- Jinchao Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenjie Liang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Yi Liu
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhitong Ren
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Dong Ci
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Jinjie Chang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- School of Life Sciences, Peking University, Beijing 100871, China
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9
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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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10
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Li Q, Lu D, Sun H, Guo J, Mo J. Tylosin toxicity in the alga Raphidocelis subcapitata revealed by integrated analyses of transcriptome and metabolome: Photosynthesis and DNA replication-coupled repair. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 239:105964. [PMID: 34534865 DOI: 10.1016/j.aquatox.2021.105964] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/19/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Tylosin (TYN) is widely used in veterinary prophylactic as a macrolide and frequently detected in the surface water. Previous studies showed that exposure to TYN caused suppression of chlorophyll biosynthesis and inhibition of photosynthesis at the physiological level, associated with reduced growth performances in algae, but the molecular mechanisms remain unknown, especially at environmental exposure levels. The present study elucidated the underlying molecular mechanism(s) of TYN toxicity in a model green alga Raphidocelis subcapitata using approaches of transcriptomics and metabolomics. Following a 7-day exposure, algal growth performances were reduced by 26.3% and 58.3% in the 3 (an environmentally realistic level) and 400 μg L-1 TYN treatment group, respectively. A total of 577 (99) and 5438 (180) differentially expressed genes (differentially accumulated metabolites) were identified in algae treated with 3 and 400 μg L-1 TYN, respectively. Signaling pathways including photosynthesis - antenna protein, porphyrin and chlorophyll metabolism, carbon fixation in photosynthetic organisms, and DNA replication were altered in the 400 μg L-1 TYN treatment, while photosynthesis and DNA replication were the shared pathways in both TYN treatments. The metabolomic data further suggest that molecular pathways related to photosynthesis, DNA replication-coupled repair and energy metabolism were impaired. Photosynthesis was identified as the most sensitive target of TYN toxicity in R. subcapitata, in contrast to protein synthesis inhibition caused by TYN in bacteria. This study provides novel mechanistic information of TYN toxicity in R. subcapitata.
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Affiliation(s)
- Qi Li
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Denglong Lu
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Haotian Sun
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China.
| | - Jiezhang Mo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China; State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China.
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11
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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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12
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Goyal M, Singh BK, Simantov K, Kaufman Y, Eshar S, Dzikowski R. An SR protein is essential for activating DNA repair in malaria parasites. J Cell Sci 2021; 134:271848. [PMID: 34291805 PMCID: PMC8435287 DOI: 10.1242/jcs.258572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/14/2021] [Indexed: 11/24/2022] Open
Abstract
Plasmodium falciparum, the parasite responsible for the deadliest form of human malaria, replicates within the erythrocytes of its host, where it encounters numerous pressures that cause extensive DNA damage, which must be repaired efficiently to ensure parasite survival. Malaria parasites, which have lost the non-homologous end joining (NHEJ) pathway for repairing DNA double-strand breaks, have evolved unique mechanisms that enable them to robustly maintain genome integrity under such harsh conditions. However, the nature of these adaptations is unknown. We show that a highly conserved RNA splicing factor, P. falciparum (Pf)SR1, plays an unexpected and crucial role in DNA repair in malaria parasites. Using an inducible and reversible system to manipulate PfSR1 expression, we demonstrate that this protein is recruited to foci of DNA damage. Although loss of PfSR1 does not impair parasite viability, the protein is essential for their recovery from DNA-damaging agents or exposure to artemisinin, the first-line antimalarial drug, demonstrating its necessity for DNA repair. These findings provide key insights into the evolution of DNA repair pathways in malaria parasites as well as the ability of the parasite to recover from antimalarial treatment. Summary: There is an unexpected role for the alternative splicing factor PfSR1 in activating the DNA damage response in the human malaria parasite Plasmodium falciparum.
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Affiliation(s)
- Manish Goyal
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Brajesh Kumar Singh
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Karina Simantov
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yotam Kaufman
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Shiri Eshar
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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13
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Nisa M, Bergis C, Pedroza-Garcia JA, Drouin-Wahbi J, Mazubert C, Bergounioux C, Benhamed M, Raynaud C. The plant DNA polymerase theta is essential for the repair of replication-associated DNA damage. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1197-1207. [PMID: 33989439 DOI: 10.1111/tpj.15295] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Safeguarding of genome integrity is a key process in all living organisms. Due to their sessile lifestyle, plants are particularly exposed to all kinds of stress conditions that could induce DNA damage. However, very few genes involved in the maintenance of genome integrity are indispensable to plants' viability. One remarkable exception is the POLQ gene, which encodes DNA polymerase theta (Pol θ), a non-replicative polymerase involved in trans-lesion synthesis during DNA replication and double-strand break (DSB) repair. The Arabidopsis tebichi (teb) mutants, deficient in Pol θ, have been reported to display severe developmental defects, leading to the conclusion that Pol θ is required for normal plant development. However, this essential role of Pol θ in plants is challenged by contradictory reports regarding the phenotypic defects of teb mutants and the recent finding that rice (Oryza sativa) null mutants develop normally. Here we show that the phenotype of teb mutants is highly variable. Taking advantage of hypomorphic mutants for the replicative DNA polymerase epsilon, which display constitutive replicative stress, we show that Pol θ allows maintenance of meristem activity when DNA replication is partially compromised. Furthermore, we found that the phenotype of Pol θ mutants can be aggravated by modifying their growth conditions, suggesting that environmental conditions impact the basal level of replicative stress and providing evidence for a link between plants' responses to adverse conditions and mechanisms involved in the maintenance of genome integrity.
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Affiliation(s)
- Maherun Nisa
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
| | - Clara Bergis
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
| | - Jose-Antonio Pedroza-Garcia
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
| | - Jeannine Drouin-Wahbi
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
| | - Christelle Mazubert
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
- Institut Universitaire de France (IUF), France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
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14
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Duan S, Hu L, Dong B, Jin HL, Wang HB. Signaling from Plastid Genome Stability Modulates Endoreplication and Cell Cycle during Plant Development. Cell Rep 2021; 32:108019. [PMID: 32783941 DOI: 10.1016/j.celrep.2020.108019] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/08/2020] [Accepted: 07/20/2020] [Indexed: 01/10/2023] Open
Abstract
Plastid-nucleus genome coordination is crucial for plastid activity, but the mechanisms remain unclear. By treating Arabidopsis plants with the organellar genome-damaging agent ciprofloxacin, we found that plastid genome instability can alter endoreplication and the cell cycle. Similar results are observed in the plastid genome instability mutants of reca1why1why3. Cell division and embryo development are disturbed in the reca1why1why3 mutant. Notably, SMR5 and SMR7 genes, which encode cell-cycle kinase inhibitors, are upregulated in plastid genome instability plants, and the mutation of SMR7 can restore the endoreplication and growth phenotype of reca1why1why3 plants. Furthermore, we establish that the DNA damage response transcription factor SOG1 mediates the alteration of endoreplication and cell cycle triggered by plastid genome instability. Finally, we demonstrate that reactive oxygen species produced in plastids are important for plastid-nucleus genome coordination. Our findings uncover a molecular mechanism for the coordination of plastid and nuclear genomes during plant growth and development.
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Affiliation(s)
- Sujuan Duan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China; Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People's Republic of China
| | - Lili Hu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China
| | - Beibei Dong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China
| | - Hong-Lei Jin
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People's Republic of China.
| | - Hong-Bin Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China; Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 510006 Guangzhou, People's Republic of China.
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15
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Bourguet P, López-González L, Gómez-Zambrano Á, Pélissier T, Hesketh A, Potok ME, Pouch-Pélissier MN, Perez M, Da Ines O, Latrasse D, White CI, Jacobsen SE, Benhamed M, Mathieu O. DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis. Genome Biol 2020; 21:283. [PMID: 33234150 PMCID: PMC7687843 DOI: 10.1186/s13059-020-02190-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications must be faithfully passed on to daughter strands. There is evidence that DNA polymerases play a role in transcriptional silencing, but the extent of their contribution and how it relates to heterochromatin maintenance is unclear. RESULTS We isolate a strong hypomorphic Arabidopsis thaliana mutant of the POL2A catalytic subunit of DNA polymerase epsilon and show that POL2A is required to stabilize heterochromatin silencing genome-wide, likely by preventing replicative stress. We reveal that POL2A inhibits DNA methylation and histone H3 lysine 9 methylation. Hence, the release of heterochromatin silencing in POL2A-deficient mutants paradoxically occurs in a chromatin context of increased levels of these two repressive epigenetic marks. At the nuclear level, the POL2A defect is associated with fragmentation of heterochromatin. CONCLUSION These results indicate that POL2A is critical to heterochromatin structure and function, and that unhindered replisome progression is required for the faithful propagation of DNA methylation throughout the cell cycle.
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Affiliation(s)
- Pierre Bourguet
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Leticia López-González
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Ángeles Gómez-Zambrano
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
- Present Address: Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Cartuja, Avda, Américo Vespucio, 49., 41092, Sevilla, Spain
| | - Thierry Pélissier
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Amy Hesketh
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Magdalena E Potok
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Marie-Noëlle Pouch-Pélissier
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Magali Perez
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Olivier Da Ines
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Charles I White
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Olivier Mathieu
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France.
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16
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Jung IJ, Ahn JW, Jung S, Hwang JE, Hong MJ, Choi HI, Kim JB. Overexpression of rice jacalin-related mannose-binding lectin (OsJAC1) enhances resistance to ionizing radiation in Arabidopsis. BMC PLANT BIOLOGY 2019; 19:561. [PMID: 31852472 PMCID: PMC6921557 DOI: 10.1186/s12870-019-2056-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/26/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Jacalin-related lectins in plants are important in defense signaling and regulate growth, development, and response to abiotic stress. We characterized the function of a rice mannose-binding jacalin-related lectin (OsJAC1) in the response to DNA damage from gamma radiation. RESULTS Time- and dose-dependent changes of OsJAC1 expression in rice were detected in response to gamma radiation. To identify OsJAC1 function, OsJAC1-overexpressing transgenic Arabidopsis plants were generated. Interestingly, OsJAC1 overexpression conferred hyper-resistance to gamma radiation in these plants. Using comparative transcriptome analysis, genes related to pathogen defense were identified among 22 differentially expressed genes in OsJAC1-overexpressing Arabidopsis lines following gamma irradiation. Furthermore, expression profiles of genes associated with the plant response to DNA damage were determined in these transgenic lines, revealing expression changes of important DNA damage checkpoint and perception regulatory components, namely MCMs, RPA, ATM, and MRE11. CONCLUSIONS OsJAC1 overexpression may confer hyper-resistance to gamma radiation via activation of DNA damage perception and DNA damage checkpoints in Arabidopsis, implicating OsJAC1 as a key player in DNA damage response in plants. This study is the first report of a role for mannose-binding jacalin-related lectin in DNA damage.
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Affiliation(s)
- In Jung Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212 Republic of Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212 Republic of Korea
| | - Sera Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212 Republic of Korea
| | - Jung Eun Hwang
- Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, 33657 Republic of Korea
| | - Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212 Republic of Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212 Republic of Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212 Republic of Korea
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17
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Abstract
Maintenance of genome integrity is a key process in all organisms. DNA polymerases (Pols) are central players in this process as they are in charge of the faithful reproduction of the genetic information, as well as of DNA repair. Interestingly, all eukaryotes possess a large repertoire of polymerases. Three protein complexes, DNA Pol α, δ, and ε, are in charge of nuclear DNA replication. These enzymes have the fidelity and processivity required to replicate long DNA sequences, but DNA lesions can block their progression. Consequently, eukaryotic genomes also encode a variable number of specialized polymerases (between five and 16 depending on the organism) that are involved in the replication of damaged DNA, DNA repair, and organellar DNA replication. This diversity of enzymes likely stems from their ability to bypass specific types of lesions. In the past 10–15 years, our knowledge regarding plant DNA polymerases dramatically increased. In this review, we discuss these recent findings and compare acquired knowledge in plants to data obtained in other eukaryotes. We also discuss the emerging links between genome and epigenome replication.
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18
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Pedroza-García JA, Nájera-Martínez M, Mazubert C, Aguilera-Alvarado P, Drouin-Wahbi J, Sánchez-Nieto S, Gualberto JM, Raynaud C, Plasencia J. Role of pyrimidine salvage pathway in the maintenance of organellar and nuclear genome integrity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:430-446. [PMID: 30317699 DOI: 10.1111/tpj.14128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/08/2018] [Indexed: 06/08/2023]
Abstract
Nucleotide biosynthesis proceeds through a de novo pathway and a salvage route. In the salvage route, free bases and/or nucleosides are recycled to generate the corresponding nucleotides. Thymidine kinase (TK) is the first enzyme in the salvage pathway to recycle thymidine nucleosides as it phosphorylates thymidine to yield thymidine monophosphate. The Arabidopsis genome contains two TK genes -TK1a and TK1b- that show similar expression patterns during development. In this work, we studied the respective roles of the two genes during early development and in response to genotoxic agents targeting the organellar or the nuclear genome. We found that the pyrimidine salvage pathway is crucial for chloroplast development and genome replication, as well as for the maintenance of its integrity, and is thus likely to play a crucial role during the transition from heterotrophy to autotrophy after germination. Interestingly, defects in TK activity could be partially compensated by supplementation of the medium with sugar, and this effect resulted from both the availability of a carbon source and the activation of the nucleotide de novo synthesis pathway, providing evidence for a compensation mechanism between two routes of nucleotide biosynthesis that depend on nutrient availability. Finally, we found differential roles of the TK1a and TK1b genes during the plant response to genotoxic stress, suggesting that different pools of nucleotides exist within the cells and are required to respond to different types of DNA damage. Altogether, our results highlight the importance of the pyrimidine salvage pathway, both during plant development and in response to genotoxic stress.
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Affiliation(s)
- José-Antonio Pedroza-García
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510 CD, Mexico
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405, Orsay, Paris, France
| | - Manuela Nájera-Martínez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510 CD, Mexico
| | - Christelle Mazubert
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405, Orsay, Paris, France
| | - Paulina Aguilera-Alvarado
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510 CD, Mexico
| | - Jeannine Drouin-Wahbi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405, Orsay, Paris, France
| | - Sobeida Sánchez-Nieto
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510 CD, Mexico
| | - José M Gualberto
- Institut de Biologie Moléculaire des Plantes, CNRS-UPR2357, Université de Strasbourg, 67084, Strasbourg, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405, Orsay, Paris, France
| | - Javier Plasencia
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510 CD, Mexico
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19
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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: 114] [Impact Index Per Article: 22.8] [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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20
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Bourbousse C, Vegesna N, Law JA. SOG1 activator and MYB3R repressors regulate a complex DNA damage network in Arabidopsis. Proc Natl Acad Sci U S A 2018; 115:E12453-E12462. [PMID: 30541889 PMCID: PMC6310815 DOI: 10.1073/pnas.1810582115] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To combat DNA damage, organisms mount a DNA damage response (DDR) that results in cell cycle regulation, DNA repair and, in severe cases, cell death. Underscoring the importance of gene regulation in this response, studies in Arabidopsis have demonstrated that all of the aforementioned processes rely on SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a NAC family transcription factor (TF) that has been functionally equated to the mammalian tumor suppressor, p53. However, the expression networks connecting SOG1 to these processes remain largely unknown and, although the DDR spans from minutes to hours, most transcriptomic data correspond to single time-point snapshots. Here, we generated transcriptional models of the DDR from GAMMA (γ)-irradiated wild-type and sog1 seedlings during a 24-hour time course using DREM, the Dynamic Regulatory Events Miner, revealing 11 coexpressed gene groups with distinct biological functions and cis-regulatory features. Within these networks, additional chromatin immunoprecipitation and transcriptomic experiments revealed that SOG1 is the major activator, directly targeting the most strongly up-regulated genes, including TFs, repair factors, and early cell cycle regulators, while three MYB3R TFs are the major repressors, specifically targeting the most strongly down-regulated genes, which mainly correspond to G2/M cell cycle-regulated genes. Together these models reveal the temporal dynamics of the transcriptional events triggered by γ-irradiation and connects these events to TFs and biological processes over a time scale commensurate with key processes coordinated in response to DNA damage, greatly expanding our understanding of the DDR.
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Affiliation(s)
- Clara Bourbousse
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Neeraja Vegesna
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037;
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
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21
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Qian J, Chen Y, Hu Y, Deng Y, Liu Y, Li G, Zou W, Zhao J. Arabidopsis replication factor C4 is critical for DNA replication during the mitotic cell cycle. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:288-303. [PMID: 29406597 DOI: 10.1111/tpj.13855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/16/2018] [Accepted: 01/23/2018] [Indexed: 06/07/2023]
Abstract
Replication factor C (RFC) is a conserved eukaryotic complex consisting of RFC1/2/3/4/5. It plays important roles in DNA replication and the cell cycle in yeast and fruit fly. However, it is not very clear how RFC subunits function in higher plants, except for the Arabidopsis (At) subunits AtRFC1 and AtRFC3. In this study, we investigated the functions of AtRFC4 and found that loss of function of AtRFC4 led to an early sporophyte lethality that initiated as early as the elongated zygote stage, all defective embryos arrested at the two- to four-cell embryo proper stage, and the endosperm possessed six to eight free nuclei. Complementation of rfc4-1/+ with AtRFC4 expression driven through the embryo-specific DD45pro and ABI3pro or the endosperm-specific FIS2pro could not completely restore the defective embryo or endosperm, whereas a combination of these three promoters in rfc4-1/+ enabled the aborted ovules to develop into viable seeds. This suggests that AtRFC4 functions simultaneously in endosperm and embryo and that the proliferation of endosperm is critical for embryo maturation. Assays of DNA content in rfc4-1/+ verified that DNA replication was disrupted in endosperm and embryo, resulting in blocked mitosis. Moreover, we observed a decreased proportion of late S-phase and M-phase cells in the rfc4-1/-FIS2;DD45;ABI3pro::AtRFC4 seedlings, suggesting that incomplete DNA replication triggered cell cycle arrest in cells of the root apical meristem. Therefore, we conclude that AtRFC4 is a crucial gene for DNA replication.
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Affiliation(s)
- Jie Qian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yueyue Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ying Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yingtian Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yang Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Gang Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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22
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Vergara Z, Gutierrez C. Emerging roles of chromatin in the maintenance of genome organization and function in plants. Genome Biol 2017; 18:96. [PMID: 28535770 PMCID: PMC5440935 DOI: 10.1186/s13059-017-1236-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus. We discuss recent discoveries regarding mechanisms that establish boundaries between chromatin states and nuclear territories. Chromatin organization is crucial for genome replication, transcriptional silencing, and DNA repair and recombination. The replication machinery is relevant for the maintenance of chromatin states, influencing DNA replication origin specification and accessibility. Current studies reinforce the idea of intimate crosstalk between chromatin features and processes involving DNA transactions.
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Affiliation(s)
- Zaida Vergara
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain.
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