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Yu G, Chen Y, Yang N, Zhang H, Zhang X, Geng Y, Zhao J, Chen Z, Dong C, Lin L, Qi J, Zhang X, Jiang X, Gao W, Cai Y, Wang X, Ding J, Xiao J, Zhou K. Apoptotic Bodies Derived from Fibroblast-Like Cells in Subcutaneous Connective Tissue Inhibit Ferroptosis in Ischaemic Flaps via the miR-339-5p/KEAP1/Nrf2 Axis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307238. [PMID: 38639443 PMCID: PMC11200024 DOI: 10.1002/advs.202307238] [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: 10/18/2023] [Revised: 03/29/2024] [Indexed: 04/20/2024]
Abstract
Preventing and treating avascular necrosis at the distal end of the flaps are critical to surgery success, but current treatments are not ideal. A recent study shows that apoptotic bodies (ABs) generated near the site of apoptosis can be taken up and promote cell proliferation. The study reveals that ABs derived from fibroblast-like cells in the subcutaneous connective tissue (FSCT cells) of skin flaps promoted ischaemic flap survival. It is also found that ABs inhibited cell death and oxidative stress and promoted M1-to-M2 polarization in macrophages. Transcriptome sequencing and protein level testing demonstrated that ABs promoted ischaemic flap survival in endothelial cells and macrophages by inhibiting ferroptosis via the KEAP1-Nrf2 axis. Furthermore, microRNA (miR) sequencing data and in vitro and in vivo experiments demonstrated that ABs inhibited KEAP1 by delivering miR-339-5p to exert therapeutic effects. In conclusion, FSCT cell-derived ABs inhibited ferroptosis, promoted the macrophage M1-to-M2 transition via the miR-339-5p/KEAP1/Nrf2 axis and promoted ischaemic flap survival. These results provide a potential therapeutic strategy to promote ischaemic flap survival by administering ABs.
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Xu Z, Qu M, Shi C, Zhang H, Chen W, Qian H, Zhang Z, Qiu J, Qian Q, Shang L. The MRE11-ATM-SOG1 DNA damage signaling pathway confers rice immunity to Xanthomonas oryzae. PLANT COMMUNICATIONS 2024; 5:100789. [PMID: 38160258 PMCID: PMC11009159 DOI: 10.1016/j.xplc.2023.100789] [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: 08/10/2023] [Revised: 11/16/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Plants are constantly exposed to microbial pathogens in the environment. One branch of innate plant immunity is mediated by cell-membrane-localized receptors, but less is known about associations between DNA damage and plant immune responses. Here, we show that rice (Oryza sativa) mesophyll cells are prone to DNA double-stranded breaks (DSBs) in response to ZJ173, a strain of Xanthomonas oryzae pv. oryzae (Xoo). The DSB signal transducer ataxia telangiectasia mutated (ATM), but not the ATM and Rad3-related branch, confers resistance against Xoo. Mechanistically, the MRE11-ATM module phosphorylates suppressor of gamma response 1 (SOG1), which activates several phenylpropanoid pathway genes and prompts downstream phytoalexin biosynthesis during Xoo infection. Intriguingly, overexpression of the topoisomerase gene TOP6A3 causes a switch from the classic non-homologous end joining (NHEJ) pathway to the alternative NHEJ and homologous recombination pathways at Xoo-induced DSBs. The enhanced ATM signaling of the alternative NHEJ pathway strengthens the SOG1-regulated phenylpropanoid pathway and thereby boosts Xoo-induced phytoalexin biosynthesis in TOP6A3-OE1 overexpression lines. Overall, the MRE11-ATM-SOG1 pathway serves as a prime example of plant-pathogen interactions that occur via host non-specific recognition. The function of TOP6-facilitated ATM signaling in the defense response makes it a promising target for breeding of rice germplasm that exhibits resistance to bacterial blight disease without a growth penalty.
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Affiliation(s)
- Zhan Xu
- Guangzhou City Academy of Agricultural Sciences, Key Laboratory of Biology, Genetics and Breeding, Guangzhou 510000, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Mingnan Qu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Chuanlin Shi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hong Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wu Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hongge Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhipeng Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jiehua Qiu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; Yazhouwan National Laboratory, No. 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China.
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Yazhouwan National Laboratory, No. 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China.
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Xu Z, Zhang J, Wang X, Essemine J, Jin J, Qu M, Xiang Y, Chen W. Cold-induced inhibition of photosynthesis-related genes integrated by a TOP6 complex in rice mesophyll cells. Nucleic Acids Res 2023; 51:1823-1842. [PMID: 36660855 PMCID: PMC9976896 DOI: 10.1093/nar/gkac1275] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 12/18/2022] [Accepted: 12/25/2022] [Indexed: 01/21/2023] Open
Abstract
Photosynthesis is the most temperature-sensitive process in the plant kingdom, but how the photosynthetic pathway responds during low-temperature exposure remains unclear. Herein, cold stress (4°C) induced widespread damage in the form DNA double-stranded breaks (DSBs) in the mesophyll cells of rice (Oryza sativa), subsequently causing a global inhibition of photosynthetic carbon metabolism (PCM) gene expression. Topoisomerase genes TOP6A3 and TOP6B were induced at 4°C and their encoded proteins formed a complex in the nucleus. TOP6A3 directly interacted with KU70 to inhibit its binding to cold-induced DSBs, which was facilitated by TOP6B, finally blocking the loading of LIG4, a component of the classic non-homologous end joining (c-NHEJ) pathway. The repression of c-NHEJ repair imposed by cold extended DSB damage signaling, thus prolonging the inhibition of photosynthesis in leaves. Furthermore, the TOP6 complex negatively regulated 13 crucial PCM genes by directly binding to their proximal promoter regions. Phenotypically, TOP6A3 overexpression exacerbated the γ-irradiation-triggered suppression of PCM genes and led to the hypersensitivity of photosynthesis parameters to cold stress, dependent on the DSB signal transducer ATM. Globally, the TOP6 complex acts as a signal integrator to control PCM gene expression and synchronize cold-induced photosynthesis inhibition, which modulates carbon assimilation rates immediately in response to changes in ambient temperature.
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Affiliation(s)
- Zhan Xu
- Guangzhou City Academy of Agricultural Sciences, Key Laboratory of Biology, Genetics and Breeding, Pazhou Dadao Rd 17-19, Haizhu District, Guangzhou 510000, China
| | - Jianxiang Zhang
- Key Laboratory of Plant Functional Genomics of Ministry of Education/Jiangsu Key Laboratory of Crop Genetics, Yangzhou University, Yangzhou 225009, China
| | - Xu Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Jemaa Essemine
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jing Jin
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mingnan Qu
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Yong Xiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Weixiong Chen
- Guangzhou City Academy of Agricultural Sciences, Key Laboratory of Biology, Genetics and Breeding, Pazhou Dadao Rd 17-19, Haizhu District, Guangzhou 510000, China
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Calvo‐Baltanás V, De Jaeger‐Braet J, Cher WY, Schönbeck N, Chae E, Schnittger A, Wijnker E. Knock-down of gene expression throughout meiosis and pollen formation by virus-induced gene silencing in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:19-37. [PMID: 35340073 PMCID: PMC9543169 DOI: 10.1111/tpj.15733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Through the inactivation of genes that act during meiosis it is possible to direct the genetic make-up of plants in subsequent generations and optimize breeding schemes. Offspring may show higher recombination of parental alleles resulting from elevated crossover (CO) incidence, or by omission of meiotic divisions, offspring may become polyploid. However, stable mutations in genes essential for recombination, or for either one of the two meiotic divisions, can have pleiotropic effects on plant morphology and line stability, for instance by causing lower fertility. Therefore, it is often favorable to temporarily change gene expression during meiosis rather than relying on stable null mutants. It was previously shown that virus-induced gene silencing (VIGS) can be used to transiently reduce CO frequencies. We asked if VIGS could also be used to modify other processes throughout meiosis and during pollen formation in Arabidopsis thaliana. Here, we show that VIGS-mediated knock-down of FIGL1, RECQ4A/B, OSD1 and QRT2 can induce (i) an increase in chiasma numbers, (ii) unreduced gametes and (iii) pollen tetrads. We further show that VIGS can target both sexes and different genetic backgrounds and can simultaneously silence different gene copies. The successful knock-down of these genes in A. thaliana suggests that VIGS can be exploited to manipulate any process during or shortly after meiosis. Hence, the transient induction of changes in inheritance patterns can be used as a powerful tool for applied research and biotechnological applications.
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Affiliation(s)
- Vanesa Calvo‐Baltanás
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6700 AAthe Netherlands
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Joke De Jaeger‐Braet
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Wei Yuan Cher
- A*STAR, Institute of Molecular and Cell Biology (IMCB)61 Biopolis DriveProteos138673Singapore
| | - Nils Schönbeck
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
- UKEMartinistrasse 5220251HamburgGermany
| | - Eunyoung Chae
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Arp Schnittger
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Erik Wijnker
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6700 AAthe Netherlands
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Verma P, Kumari P, Negi S, Yadav G, Gaur V. Holliday junction resolution by At-HIGLE: an SLX1 lineage endonuclease from Arabidopsis thaliana with a novel in-built regulatory mechanism. Nucleic Acids Res 2022; 50:4630-4646. [PMID: 35412622 PMCID: PMC9071465 DOI: 10.1093/nar/gkac239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/24/2022] [Accepted: 04/01/2022] [Indexed: 12/14/2022] Open
Abstract
Holliday junction is the key homologous recombination intermediate, resolved by structure-selective endonucleases (SSEs). SLX1 is the most promiscuous SSE of the GIY-YIG nuclease superfamily. In fungi and animals, SLX1 nuclease activity relies on a non-enzymatic partner, SLX4, but no SLX1-SLX4 like complex has ever been characterized in plants. Plants exhibit specialized DNA repair and recombination machinery. Based on sequence similarity with the GIY-YIG nuclease domain of SLX1 proteins from fungi and animals, At-HIGLE was identified to be a possible SLX1 like nuclease from plants. Here, we elucidated the crystal structure of the At-HIGLE nuclease domain from Arabidopsis thaliana, establishing it as a member of the SLX1-lineage of the GIY-YIG superfamily with structural changes in DNA interacting regions. We show that At-HIGLE can process branched-DNA molecules without an SLX4 like protein. Unlike fungal SLX1, At-HIGLE exists as a catalytically active homodimer capable of generating two coordinated nicks during HJ resolution. Truncating the extended C-terminal region of At-HIGLE increases its catalytic activity, changes the nicking pattern, and monomerizes At-HIGLE. Overall, we elucidated the first structure of a plant SLX1-lineage protein, showed its HJ resolving activity independent of any regulatory protein, and identified an in-built novel regulatory mechanism engaging its C-terminal region.
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Affiliation(s)
- Prabha Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Poonam Kumari
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shreya Negi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Gitanjali Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vineet Gaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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M-Hamvas M, Vasas G, Beyer D, Nagylaki E, Máthé C. Microcystin-LR, a Cyanobacterial Toxin, Induces DNA Strand Breaks Correlated with Changes in Specific Nuclease and Protease Activities in White Mustard ( Sinapis alba) Seedlings. PLANTS 2021; 10:plants10102045. [PMID: 34685854 PMCID: PMC8537482 DOI: 10.3390/plants10102045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/04/2022]
Abstract
There is increasing evidence for the induction of programmed cell death (PCD) in vascular plants by the cyanobacterial toxin microcystin-LR (MC-LR). Our aim was to detect the occurrence of PCD-related DNA strand breaks and their possible connections to specific nuclease and protease activities. DNA breaks were studied by the deoxynucleotidyl transferase mediated dUTP nick end labeling (TUNEL) method in the photoperiodically grown dicot model of white mustard (Sinapis alba). In-gel nuclease and protease activity assays showed changes in the activities of specific isoenzymes during treatments with MC-LR. Strand breaks occurred both in the developing root epidermis and cortex. Several isoenzyme activities were related to these breaks, for example: an increase in the activity of neutral 80–75 kDa, acidic high MW (100–120 kDa) and, most importantly, an increase in the activity of neutral 26–20 kDa nucleases, all of them having single-stranded DNA cleaving (SSP nuclease) activities. Increases in the activities of alkaline proteases in the 61–41 kDa range were also detected and proved to be in relation with MC-LR-induced PCD. This is one of the first pieces of evidence on the correlation of PCD-related DNA strand breaks with specific hydrolase activities in a model dicot treated with a cyanobacterial toxin known to have environmental importance.
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Verma P, Tandon R, Yadav G, Gaur V. Structural Aspects of DNA Repair and Recombination in Crop Improvement. Front Genet 2020; 11:574549. [PMID: 33024442 PMCID: PMC7516265 DOI: 10.3389/fgene.2020.574549] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
The adverse effects of global climate change combined with an exponentially increasing human population have put substantial constraints on agriculture, accelerating efforts towards ensuring food security for a sustainable future. Conventional plant breeding and modern technologies have led to the creation of plants with better traits and higher productivity. Most crop improvement approaches (conventional breeding, genome modification, and gene editing) primarily rely on DNA repair and recombination (DRR). Studying plant DRR can provide insights into designing new strategies or improvising the present techniques for crop improvement. Even though plants have evolved specialized DRR mechanisms compared to other eukaryotes, most of our insights about plant-DRRs remain rooted in studies conducted in animals. DRR mechanisms in plants include direct repair, nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), non-homologous end joining (NHEJ) and homologous recombination (HR). Although each DRR pathway acts on specific DNA damage, there is crosstalk between these. Considering the importance of DRR pathways as a tool in crop improvement, this review focuses on a general description of each DRR pathway, emphasizing on the structural aspects of key DRR proteins. The review highlights the gaps in our understanding and the importance of studying plant DRR in the context of crop improvement.
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Affiliation(s)
- Prabha Verma
- National Institute of Plant Genome Research, New Delhi, India
| | - Reetika Tandon
- National Institute of Plant Genome Research, New Delhi, India
| | - Gitanjali Yadav
- National Institute of Plant Genome Research, New Delhi, India
| | - Vineet Gaur
- National Institute of Plant Genome Research, New Delhi, India
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9
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Zhang J, Si J, Gan L, Zhou R, Guo M, Zhang H. Harnessing the targeting potential of differential radiobiological effects of photon versus particle radiation for cancer treatment. J Cell Physiol 2020; 236:1695-1711. [PMID: 32691425 DOI: 10.1002/jcp.29960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/09/2020] [Indexed: 01/04/2023]
Abstract
Radiotherapy is one of the major modalities for malignancy treatment. High linear energy transfer (LET) charged-particle beams, like proton and carbon ions, exhibit favourable depth-dose distributions and radiobiological enhancement over conventional low-LET photon irradiation, thereby marking a new era in high precision medicine. Tumour cells have developed multicomponent signal transduction networks known as DNA damage responses (DDRs), which initiate cell-cycle checkpoints and induce double-strand break (DSB) repairs in the nucleus by nonhomologous end joining or homologous recombination pathways, to manage ionising radiation (IR)-induced DNA lesions. DNA damage induction and DSB repair pathways are reportedly dependent on the quality of radiation delivered. In this review, we summarise various types of DNA lesion and DSB repair mechanisms, upon irradiation with low and high-LET radiation, respectively. We also analyse factors influencing DNA repair efficiency. Inhibition of DNA damage repair pathways and dysfunctional cell-cycle checkpoint sensitises tumour cells to IR. Radio-sensitising agents, including DNA-PK inhibitors, Rad51 inhibitors, PARP inhibitors, ATM/ATR inhibitors, chk1 inhibitors, wee1 kinase inhibitors, Hsp90 inhibitors, and PI3K/AKT/mTOR inhibitors have been found to enhance cell killing by IR through interference with DDRs, cell-cycle arrest, or other cellular processes. The cotreatment of these inhibitors with IR may represent a promising therapeutic strategy for cancer.
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Affiliation(s)
- Jinhua Zhang
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Si
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lu Gan
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rong Zhou
- Research Center for Ecological Impacts and Environmental Health Effects of Toxic and Hazardous Chemicals, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, China
| | - Menghuan Guo
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Hong Zhang
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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DNA Helicases as Safekeepers of Genome Stability in Plants. Genes (Basel) 2019; 10:genes10121028. [PMID: 31835565 PMCID: PMC6947026 DOI: 10.3390/genes10121028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 02/07/2023] Open
Abstract
Genetic information of all organisms is coded in double-stranded DNA. DNA helicases are essential for unwinding this double strand when it comes to replication, repair or transcription of genetic information. In this review, we will focus on what is known about a variety of DNA helicases that are required to ensure genome stability in plants. Due to their sessile lifestyle, plants are especially exposed to harmful environmental factors. Moreover, many crop plants have large and highly repetitive genomes, making them absolutely dependent on the correct interplay of DNA helicases for safeguarding their stability. Although basic features of a number of these enzymes are conserved between plants and other eukaryotes, a more detailed analysis shows surprising peculiarities, partly also between different plant species. This is additionally of high relevance for plant breeding as a number of these helicases are also involved in crossover control during meiosis and influence the outcome of different approaches of CRISPR/Cas based plant genome engineering. Thus, gaining knowledge about plant helicases, their interplay, as well as the manipulation of their pathways, possesses the potential for improving agriculture. In the long run, this might even help us cope with the increasing obstacles of climate change threatening food security in completely new ways.
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Fayos I, Mieulet D, Petit J, Meunier AC, Périn C, Nicolas A, Guiderdoni E. Engineering meiotic recombination pathways in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2062-2077. [PMID: 31199561 PMCID: PMC6790369 DOI: 10.1111/pbi.13189] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 06/01/2019] [Accepted: 06/05/2019] [Indexed: 05/02/2023]
Abstract
In the last 15 years, outstanding progress has been made in understanding the function of meiotic genes in the model dicot and monocot plants Arabidopsis and rice (Oryza sativa L.), respectively. This knowledge allowed to modulate meiotic recombination in Arabidopsis and, more recently, in rice. For instance, the overall frequency of crossovers (COs) has been stimulated 2.3- and 3.2-fold through the inactivation of the rice FANCM and RECQ4 DNA helicases, respectively, two genes involved in the repair of DNA double-strand breaks (DSBs) as noncrossovers (NCOs) of the Class II crossover pathway. Differently, the programmed induction of DSBs and COs at desired sites is currently explored by guiding the SPO11-1 topoisomerase-like transesterase, initiating meiotic recombination in all eukaryotes, to specific target regions of the rice genome. Furthermore, the inactivation of 3 meiosis-specific genes, namely PAIR1, OsREC8 and OsOSD1, in the Mitosis instead of Meiosis (MiMe) mutant turned rice meiosis into mitosis, thereby abolishing recombination and achieving the first component of apomixis, apomeiosis. The successful translation of Arabidopsis results into a crop further allowed the implementation of two breakthrough strategies that triggered parthenogenesis from the MiMe unreduced clonal egg cell and completed the second component of diplosporous apomixis. Here, we review the most recent advances in and future prospects of the manipulation of meiotic recombination in rice and potentially other major crops, all essential for global food security.
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Affiliation(s)
- Ian Fayos
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Delphine Mieulet
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Julie Petit
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Anne Cécile Meunier
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Christophe Périn
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
| | - Alain Nicolas
- Institut Curie, CNRS UMR 3244University PSLParisFrance
- MeiogenixParisFrance
| | - Emmanuel Guiderdoni
- CiradUMR AGAPMontpellierFrance
- Université de MontpellierCirad-Inra-Montpellier SupAgroMontpellierFrance
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Sheteiwy MS, An J, Yin M, Jia X, Guan Y, He F, Hu J. Cold plasma treatment and exogenous salicylic acid priming enhances salinity tolerance of Oryza sativa seedlings. PROTOPLASMA 2019; 256:79-99. [PMID: 29984388 DOI: 10.1007/s00709-018-1279-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/15/2018] [Indexed: 05/06/2023]
Abstract
The present study was designed to highlight the effects of cold plasma (10 kV) treatment and priming with 2 mM salicylic acid (SA) and their combination (10 kV of plasma + 2 mM SA) on the physiological parameters and metabolism of two cultivars of Oryza sativa, i.e., Zhu Liang You 06 (ZY) and Qian You No. 1 (QY), under salinity stress (150 mM NaCl) and normal growth condition (0 mM NaCl). Seed germination and seedling growth were enhanced by SA priming and cold plasma treatment either alone or in combination under salinity stress. Photosynthetic pigments, photosynthetic gas exchange, and chlorophyll fluorescence were improved by cold plasma treatment and SA priming under salinity stress as compared to the untreated seeds. The activities of antioxidant enzymes were significantly improved by the combination of SA priming and cold plasma treatment in both cultivars under salinity stress. There were rapid changes in the cellular content of sodium (Na+) and calcium (Ca+), where the plants grown under saline conditions accumulate more Na+ and less Ca+ contents resulting in ionic imbalances. Interestingly, cold plasma and SA treatments diminished this action by reducing Na+ accumulation and increasing K+ and Ca+ contents in the plant cell under salinity stress. The activities of enzymes involved in secondary metabolism assimilation were up-regulated with cold plasma and SA priming either alone or combination under salinity stress. An increase in reactive oxygen species (ROS) accumulation and malondialdehyde (MDA) content was also observed under salinity stress condition. On contrast, seed treated with SA and plasma alone or combined resulted in a significant decrease in ROS and MDA contents under salinity stress. Our results indicated that SA priming and cold plasma treatment either alone or combined improved plant uptake of nutrients in both cultivars under stress conditions. The ultrastructural changes were observed to be more prominent in ZY than QY cultivar. Plants without SA priming or cold plasma treatments have a big vacuole due to the movement of ions into the vacuole directly from the apoplast into the vacuole through membrane vesiculation leading to membrane destabilization. However, SA priming and cold plasma treatment alone or combined helped the plants to recover their cell turgidity under salinity stress.
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Affiliation(s)
- Mohamed S Sheteiwy
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Department of Agronomy, Faculty of Agriculture, Mansoura University, Mansoura, 35516, Egypt
| | - Jianyu An
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Mengqi Yin
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaowen Jia
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yajing Guan
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Fei He
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jin Hu
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Mieulet D, Aubert G, Bres C, Klein A, Droc G, Vieille E, Rond-Coissieux C, Sanchez M, Dalmais M, Mauxion JP, Rothan C, Guiderdoni E, Mercier R. Unleashing meiotic crossovers in crops. NATURE PLANTS 2018; 4:1010-1016. [PMID: 30478361 DOI: 10.1038/s41477-018-0311-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/17/2018] [Indexed: 05/21/2023]
Abstract
Improved plant varieties are important in our attempts to face the challenges of a growing human population and limited planet resources. Plant breeding relies on meiotic crossovers to combine favourable alleles into elite varieties1. However, meiotic crossovers are relatively rare, typically one to three per chromosome2, limiting the efficiency of the breeding process and related activities such as genetic mapping. Several genes that limit meiotic recombination were identified in the model species Arabidopsis thaliana2. Mutation of these genes in Arabidopsis induces a large increase in crossover frequency. However, it remained to be demonstrated whether crossovers could also be increased in crop species hybrids. We explored the effects of mutating the orthologues of FANCM3, RECQ44 or FIGL15 on recombination in three distant crop species, rice (Oryza sativa), pea (Pisum sativum) and tomato (Solanum lycopersicum). We found that the single recq4 mutation increases crossovers about three-fold in these crops, suggesting that manipulating RECQ4 may be a universal tool for increasing recombination in plants. Enhanced recombination could be used with other state-of-the-art technologies such as genomic selection, genome editing or speed breeding6 to enhance the pace and efficiency of plant improvement.
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Affiliation(s)
- Delphine Mieulet
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Gregoire Aubert
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Cecile Bres
- UMR 1332 BFP, INRA, Université Bordeaux, Villenave d'Ornon, France
| | - Anthony Klein
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Emilie Vieille
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Celine Rond-Coissieux
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Myriam Sanchez
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Marion Dalmais
- Institute of Plant Sciences, Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
| | | | | | - Emmanuel Guiderdoni
- CIRAD, UMR AGAP, Montpellier, France
- Université Montpellier, CIRAD, INRA Montpellier SupAgro, Montpellier, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Université Paris-Saclay, Versailles, France.
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Wiedemann G, van Gessel N, Köchl F, Hunn L, Schulze K, Maloukh L, Nogué F, Decker EL, Hartung F, Reski R. RecQ Helicases Function in Development, DNA Repair, and Gene Targeting in Physcomitrella patens. THE PLANT CELL 2018; 30:717-736. [PMID: 29514942 PMCID: PMC5894843 DOI: 10.1105/tpc.17.00632] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/16/2018] [Accepted: 03/06/2018] [Indexed: 05/18/2023]
Abstract
RecQ DNA helicases are genome surveillance proteins found in all kingdoms of life. They are characterized best in humans, as mutations in RecQ genes lead to developmental abnormalities and diseases. To better understand RecQ functions in plants we concentrated on Arabidopsis thaliana and Physcomitrella patens, the model species predominantly used for studies on DNA repair and gene targeting. Phylogenetic analysis of the six P. patens RecQ genes revealed their orthologs in humans and plants. Because Arabidopsis and P. patens differ in their RecQ4 and RecQ6 genes, reporter and deletion moss mutants were generated and gene functions studied in reciprocal cross-species and cross-kingdom approaches. Both proteins can be found in meristematic moss tissues, although at low levels and with distinct expression patterns. PpRecQ4 is involved in embryogenesis and in subsequent development as demonstrated by sterility of ΔPpRecQ4 mutants and by morphological aberrations. Additionally, ΔPpRecQ4 displays an increased sensitivity to DNA damages and an increased rate of gene targeting. Therefore, we conclude that PpRecQ4 acts as a repressor of recombination. In contrast, PpRecQ6 is not obviously important for moss development or DNA repair but does function as a potent enhancer of gene targeting.
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Affiliation(s)
- Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Fabian Köchl
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Lisa Hunn
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Katrin Schulze
- Julius Kuehn Institute, Institute for Biosafety in Plant Biotechnology, 06484 Quedlinburg, Germany
| | - Lina Maloukh
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Frank Hartung
- Julius Kuehn Institute, Institute for Biosafety in Plant Biotechnology, 06484 Quedlinburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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15
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Dantas AF, Lopes RM, Fascineli ML, José SCBR, Pádua JG, Gimenes MA, Grisolia CK. Comet and cytogenetic tests as tools for evaluating genomic instability in seeds of Oryza sativa L. and Phaseolus vulgaris L. from gene banks. Genet Mol Biol 2018; 41:145-153. [PMID: 29658968 PMCID: PMC5901492 DOI: 10.1590/1678-4685-gmb-2017-0020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 09/11/2017] [Indexed: 11/29/2022] Open
Abstract
This study aimed to assess the feasibility of comet and cytogenetic tests as tools for evaluating genomic instability in seeds of Oryza sativa L. (rice) and Phaseolus vulgaris (beans) L. from gene banks. Rice and beans were exposed to methyl methanesulfonate (MMS) as a reference DNA damaging agent. Seeds of two accessions of rice and beans were obtained from Embrapa Rice and Beans - Brazil. Seed groups were imbibed in three concentrations of MMS for three periods of time to carry out cytogenetic tests, and for one period for the comet test. At concentrations of 10 and 15 mg/L, MMS induced cytotoxic and/or mutagenic effects in the meristematic cells of roots from all the accessions of both species. In the comet test, MMS induced genotoxic effects at all the concentrations in the evaluated accessions of rice and beans, except in one accession of beans at the lowest concentration (5 mg/L). Both species showed sensitivity to MMS. The comet test can be proposed for the measurement of genomic instability in accessions of rice and beans in gene banks, as being more sensitive than the cytogenetic tests used.
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Affiliation(s)
- Alisson F Dantas
- Laboratório de Genética Toxicológica, Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Renata M Lopes
- Departmento de Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Maria L Fascineli
- Laboratório de Genética Toxicológica, Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | | | - Juliano G Pádua
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Marcos A Gimenes
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Cesar K Grisolia
- Laboratório de Genética Toxicológica, Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
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16
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Pan X, Fang Y, Yang X, Zheng D, Chen L, Wang L, Xiao J, Wang XE, Wang K, Cheng Z, Yu H, Zhang W. Chromatin states responsible for the regulation of differentially expressed genes under 60Co~γ ray radiation in rice. BMC Genomics 2017; 18:778. [PMID: 29025389 PMCID: PMC5639768 DOI: 10.1186/s12864-017-4172-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/05/2017] [Indexed: 11/24/2022] Open
Abstract
Background The role of histone modifications in the DNA damage response has been extensively studied in non-plant systems, including mammals and yeast. However, there is a lack of detailed evidence showing how chromatin dynamics, either an individual mark or combined chromatin states, participate in regulating differentially expressed genes in the plant DNA damage response. Results In this study, we used RNA-seq and ChIP-seq to show that differentially expressed genes (DEGs), in response to ionizing radiation (IR), might be involved in different pathways responsible for the DNA damage response. Moreover, chromatin structures associated with promoters, exons and intergenic regions are significantly affected by IR. Most importantly, either an individual mark or a certain chromatin state was found to be highly correlated with the expression of up-regulated genes. In contrast, only the chromatin states, as opposed to any individual marks tested, are related to the expression of the down-regulated genes. Conclusions Our findings demonstrate that IR-related DEGs are modulated by distinct epigenetic mechanisms. Either chromatin states or distinct histone dynamics may act sequentially or in combination in regulating up-regulated genes, but the complex chromatin structure is mainly responsible for the expression of down-regulated genes. Thus, this study provides new insights into how up- and down-regulated genes are epigenetically regulated at the chromatin levels, thereby helping us to understand distinct epigenetic mechanisms that function in the plant DNA damage response. Electronic supplementary material The online version of this article (10.1186/s12864-017-4172-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiucai Pan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Yuan Fang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Xueming Yang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Dongyang Zheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Lifen Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Lei Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Jin Xiao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Xiu-E Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Kai Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, Fujian, 35002, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hengxiu Yu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China. .,JiangSu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China.
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17
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Nair PMG, Chung IM. Evaluation of stress effects of copper oxide nanoparticles in Brassica napus L. seedlings. 3 Biotech 2017; 7:293. [PMID: 28868220 PMCID: PMC5577373 DOI: 10.1007/s13205-017-0929-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 08/22/2017] [Indexed: 10/19/2022] Open
Abstract
Rapid growth of nanotechnology has enabled the production and use of engineered nanoparticles (ENPs) in several industries as well as in agriculture areas. This has raised ecotoxicological concerns due to the release of ENPs to the environment. In the present study, we investigated the effects of interactions of copper oxide nanoparticles (CuO NPs) on physiological, biochemical, and molecular indices in seedlings of an important oil seed crop Brassica napus L. The seedlings were treated with 0, 20, 50, 100, 200, 400, and 500 mg/L of CuO NPs for 14 days in half-strength semi-solid Murashige and Skoog medium. The CuO NPs treatment significantly reduced shoot and root growth as well as plant biomass. Shortening and thickening of primary and lateral roots and inhibition of lateral root growth was observed at higher concentrations. An increase in reactive oxygen species generation, and malondialdehyde accumulation was observed. Histochemical staining of roots with propidium iodide and aniline blue indicated cell death and callose formation in roots. Transcriptional modulation of genes related to oxidative stress viz. CuZn superoxide dismutase, catalase, and ascorbate peroxidase was observed. Element content analysis showed an increase in Cu content and decrease in Fe, Mn, and Zn contents. Overall, exposure to CuO NPs caused oxidative injury, cell death, callose formation, and decreased the micro nutrient contents in B. napus seedlings.
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Affiliation(s)
- Prakash M. Gopalakrishnan Nair
- Department of Applied Bioscience, College of Life and Environmental Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029 South Korea
| | - Ill Min Chung
- Department of Applied Bioscience, College of Life and Environmental Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029 South Korea
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18
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Tripathi AK, Pareek A, Singla-Pareek SL. TUNEL Assay to Assess Extent of DNA Fragmentation and Programmed Cell Death in Root Cells under Various Stress Conditions. Bio Protoc 2017; 7:e2502. [PMID: 34541167 DOI: 10.21769/bioprotoc.2502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/02/2017] [Accepted: 07/13/2017] [Indexed: 11/02/2022] Open
Abstract
DNA damage is one of the common consequences of exposure to various stress conditions. Different methods have been developed to accurately assess DNA damage and fragmentation in cells and tissues exposed to different stress agents. However, owing to the presence of firm cellulosic cell wall and phenolics, plant cells and tissues are not easily amenable to be subjected to these assays. Here, we describe an optimized TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling) assay-based protocol to determine the extent of DNA fragmentation and programmed cell death in plant root cells subjected to various stress conditions. The method described here has the advantages of simplicity, reliability and reproducibility.
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Affiliation(s)
- Amit K Tripathi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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19
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Olivier M, Da Ines O, Amiard S, Serra H, Goubely C, White CI, Gallego ME. The Structure-Specific Endonucleases MUS81 and SEND1 Are Essential for Telomere Stability in Arabidopsis. THE PLANT CELL 2016; 28:74-86. [PMID: 26704385 PMCID: PMC4746687 DOI: 10.1105/tpc.15.00898] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/23/2015] [Indexed: 05/02/2023]
Abstract
Structure-specific endonucleases act to repair potentially toxic structures produced by recombination and DNA replication, ensuring proper segregation of the genetic material to daughter cells during mitosis and meiosis. Arabidopsis thaliana has two putative homologs of the resolvase (structure-specific endonuclease): GEN1/Yen1. Knockout of resolvase genes GEN1 and SEND1, individually or together, has no detectable effect on growth, fertility, or sensitivity to DNA damage. However, combined absence of the endonucleases MUS81 and SEND1 results in severe developmental defects, spontaneous cell death, and genome instability. A similar effect is not seen in mus81 gen1 plants, which develop normally and are fertile. Absence of RAD51 does not rescue mus81 send1, pointing to roles of these proteins in DNA replication rather than DNA break repair. The enrichment of S-phase histone γ-H2AX foci and a striking loss of telomeric DNA in mus81 send1 further support this interpretation. SEND1 has at most a minor role in resolution of the Holliday junction but acts as an essential backup to MUS81 for resolution of toxic replication structures to ensure genome stability and to maintain telomere integrity.
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Affiliation(s)
- Margaux Olivier
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Olivier Da Ines
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Simon Amiard
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Heïdi Serra
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Chantal Goubely
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Charles I White
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Maria E Gallego
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
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20
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Gopalakrishnan Nair PM, Chung IM. Biochemical, anatomical and molecular level changes in cucumber (Cucumis sativus) seedlings exposed to copper oxide nanoparticles. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0193] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Donà M, Mittelsten Scheid O. DNA Damage Repair in the Context of Plant Chromatin. PLANT PHYSIOLOGY 2015; 168:1206-18. [PMID: 26089404 PMCID: PMC4528755 DOI: 10.1104/pp.15.00538] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/17/2015] [Indexed: 05/03/2023]
Abstract
The integrity of DNA molecules is constantly challenged. All organisms have developed mechanisms to detect and repair multiple types of DNA lesions. The basic principles of DNA damage repair (DDR) in prokaryotes and unicellular and multicellular eukaryotes are similar, but the association of DNA with nucleosomes in eukaryotic chromatin requires mechanisms that allow access of repair enzymes to the lesions. This is achieved by chromatin-remodeling factors, and their necessity for efficient DDR has recently been demonstrated for several organisms and repair pathways. Plants share many features of chromatin organization and DNA repair with fungi and animals, but they differ in other, important details, which are both interesting and relevant for our understanding of genome stability and genetic diversity. In this Update, we compare the knowledge of the role of chromatin and chromatin-modifying factors during DDR in plants with equivalent systems in yeast and humans. We emphasize plant-specific elements and discuss possible implications.
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Affiliation(s)
- Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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22
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Santos CLV, Pourrut B, Ferreira de Oliveira JMP. The use of comet assay in plant toxicology: recent advances. Front Genet 2015; 6:216. [PMID: 26175750 PMCID: PMC4485349 DOI: 10.3389/fgene.2015.00216] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 06/02/2015] [Indexed: 12/13/2022] Open
Abstract
The systematic study of genotoxicity in plants induced by contaminants and other stress agents has been hindered to date by the lack of reliable and robust biomarkers. The comet assay is a versatile and sensitive method for the evaluation of DNA damages and DNA repair capacity at single-cell level. Due to its simplicity and sensitivity, and the small number of cells required to obtain robust results, the use of plant comet assay has drastically increased in the last decade. For years its use was restricted to a few model species, e.g., Allium cepa, Nicotiana tabacum, Vicia faba, or Arabidopsis thaliana but this number largely increased in the last years. Plant comet assay has been used to study the genotoxic impact of radiation, chemicals including pesticides, phytocompounds, heavy metals, nanoparticles or contaminated complex matrices. Here we will review the most recent data on the use of this technique as a standard approach for studying the genotoxic effects of different stress conditions on plants. Also, we will discuss the integration of information provided by the comet assay with other DNA-damage indicators, and with cellular responses including oxidative stress, cell division or cell death. Finally, we will focus on putative relations between transcripts related with DNA damage pathways, DNA replication and repair, oxidative stress and cell cycle progression that have been identified in plant cells with comet assays demonstrating DNA damage.
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Affiliation(s)
| | - Bertrand Pourrut
- Laboratoire Génie Civil et géo-Environnement - Groupe ISA Lille, France
| | - José M P Ferreira de Oliveira
- Laboratory of Biotechnology and Cytometry, Centre for Environmental and Marine Studies, University of Aveiro Aveiro, Portugal
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23
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Takahashi S, Kojo KH, Kutsuna N, Endo M, Toki S, Isoda H, Hasezawa S. Differential responses to high- and low-dose ultraviolet-B stress in tobacco Bright Yellow-2 cells. FRONTIERS IN PLANT SCIENCE 2015; 6:254. [PMID: 25954287 PMCID: PMC4404814 DOI: 10.3389/fpls.2015.00254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/31/2015] [Indexed: 05/14/2023]
Abstract
Ultraviolet (UV)-B irradiation leads to DNA damage, cell cycle arrest, growth inhibition, and cell death. To evaluate the UV-B stress-induced changes in plant cells, we developed a model system based on tobacco Bright Yellow-2 (BY-2) cells. Both low-dose UV-B (low UV-B: 740 J m(-2)) and high-dose UV-B (high UV-B: 2960 J m(-2)) inhibited cell proliferation and induced cell death; these effects were more pronounced at high UV-B. Flow cytometry showed cell cycle arrest within 1 day after UV-B irradiation; neither low- nor high-UV-B-irradiated cells entered mitosis within 12 h. Cell cycle progression was gradually restored in low-UV-B-irradiated cells but not in high-UV-B-irradiated cells. UV-A irradiation, which activates cyclobutane pyrimidine dimer (CPD) photolyase, reduced inhibition of cell proliferation by low but not high UV-B and suppressed high-UV-B-induced cell death. UV-B induced CPD formation in a dose-dependent manner. The amounts of CPDs decreased gradually within 3 days in low-UV-B-irradiated cells, but remained elevated after 3 days in high-UV-B-irradiated cells. Low UV-B slightly increased the number of DNA single-strand breaks detected by the comet assay at 1 day after irradiation, and then decreased at 2 and 3 days after irradiation. High UV-B increased DNA fragmentation detected by the terminal deoxynucleotidyl transferase dUTP nick end labeling assay 1 and 3 days after irradiation. Caffeine, an inhibitor of ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) checkpoint kinases, reduced the rate of cell death in high-UV-B-irradiated cells. Our data suggest that low-UV-B-induced CPDs and/or DNA strand-breaks inhibit DNA replication and proliferation of BY-2 cells, whereas larger contents of high-UV-B-induced CPDs and/or DNA strand-breaks lead to cell death.
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Affiliation(s)
- Shinya Takahashi
- Department of Integrated Biosciences, Graduated School of Frontier Sciences, The University of TokyoKashiwa, Japan
- Alliance for Research on North Africa, University of TsukubaTsukuba, Japan
- Ph. D. Program in Life Science Innovation, University of TsukubaTsukuba, Japan
| | - Kei H. Kojo
- Department of Integrated Biosciences, Graduated School of Frontier Sciences, The University of TokyoKashiwa, Japan
- LPixel Inc.Bunkyo-ku, Japan
| | - Natsumaro Kutsuna
- Department of Integrated Biosciences, Graduated School of Frontier Sciences, The University of TokyoKashiwa, Japan
- LPixel Inc.Bunkyo-ku, Japan
| | - Masaki Endo
- Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Seiichi Toki
- Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Hiroko Isoda
- Alliance for Research on North Africa, University of TsukubaTsukuba, Japan
- Ph. D. Program in Life Science Innovation, University of TsukubaTsukuba, Japan
| | - Seiichiro Hasezawa
- Department of Integrated Biosciences, Graduated School of Frontier Sciences, The University of TokyoKashiwa, Japan
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Nair PMG, Chung IM. Physiological and molecular level effects of silver nanoparticles exposure in rice (Oryza sativa L.) seedlings. CHEMOSPHERE 2014; 112:105-13. [PMID: 25048895 DOI: 10.1016/j.chemosphere.2014.03.056] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 02/05/2014] [Accepted: 03/19/2014] [Indexed: 05/04/2023]
Abstract
The physiological and molecular level changes of silver nanoparticles (AgNPs) exposure were investigated in rice (Oryza sativa L.) seedlings. The seedlings were exposed to different concentrations of (0, 0.2, 0.5 and 1 mg L(-1)) AgNPs for one week. Significant reduction in root elongation, shoot and root fresh weights, total chlorophyll and carotenoids contents were observed. Exposure to 0.5 and 1 mg L(-1) of AgNPs caused significant increase in hydrogen peroxide formation and lipid peroxidation in shoots and roots, increased foliar proline accumulation and decreased sugar contents. AgNPs exposure resulted in a dose dependant increase in reactive oxygen species generation and also caused cytotoxicity as evidenced by increased dihydroethidium, 3'-(p-hydroxyphenyl) fluorescein and propidium iodide fluorescence. Tetramethylrhodamine methyl ester assay showed decreased mitochondrial membrane potential with increasing concentrations of AgNPs exposure in roots. Real Time PCR analysis showed differential transcription of genes related to oxidative stress tolerance viz. FSD1, MSD1, CSD1, CSD2, CATa, CATb, CATc, APXa and APXb in shoots and roots of rice seedlings. The overall results suggest that exposure to AgNPs caused significant physiological and molecular level changes, oxidative stress and also resulted in the induction oxidative stress tolerance mechanisms in rice seedlings.
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Affiliation(s)
- Prakash M Gopalakrishnan Nair
- Department of Applied Biosciences, College of Life and Environmental Sciences, Konkuk University, Seoul, South Korea
| | - Ill Min Chung
- Department of Applied Biosciences, College of Life and Environmental Sciences, Konkuk University, Seoul, South Korea.
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Knoll A, Schröpfer S, Puchta H. The RTR complex as caretaker of genome stability and its unique meiotic function in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:33. [PMID: 24575106 PMCID: PMC3921566 DOI: 10.3389/fpls.2014.00033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/25/2014] [Indexed: 05/02/2023]
Abstract
The RTR complex consisting of a RecQ helicase, a type IA topoisomerase and the structural protein RMI1 is involved in the processing of DNA recombination intermediates in all eukaryotes. In Arabidopsis thaliana the complex partners RECQ4A, topoisomerase 3α and RMI1 have been shown to be involved in DNA repair and in the suppression of homologous recombination in somatic cells. Interestingly, mutants of AtTOP3A and AtRMI1 are also sterile due to extensive chromosome breakage in meiosis I, a phenotype that seems to be specific for plants. Although both proteins are essential for meiotic recombination it is still elusive on what kind of intermediates they are acting on. Recent data indicate that the pattern of non-crossover (NCO)-associated meiotic gene conversion (GC) differs between plants and other eukaryotes, as less NCOs in comparison to crossovers (CO) could be detected in Arabidopsis. This indicates that NCOs happen either more rarely in plants or that the conversion tract length is significantly shorter than in other organisms. As the TOP3α/RMI1-mediated dissolution of recombination intermediates results exclusively in NCOs, we suggest that the peculiar GC pattern found in plants is connected to the unique role, members of the RTR complex play in plant meiosis.
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Affiliation(s)
| | | | - Holger Puchta
- *Correspondence: Holger Puchta, Botanical Institute II, Karlsruhe Institute of Technology, Hertzstraße 16, 76187 Karlsruhe, Germany e-mail:
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Schröpfer S, Kobbe D, Hartung F, Knoll A, Puchta H. Defining the roles of the N-terminal region and the helicase activity of RECQ4A in DNA repair and homologous recombination in Arabidopsis. Nucleic Acids Res 2013; 42:1684-97. [PMID: 24174542 PMCID: PMC3919593 DOI: 10.1093/nar/gkt1004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RecQ helicases are critical for the maintenance of genomic stability. The Arabidopsis RecQ helicase RECQ4A is the functional counterpart of human BLM, which is mutated in the genetic disorder Bloom’s syndrome. RECQ4A performs critical roles in regulation of homologous recombination (HR) and DNA repair. Loss of RECQ4A leads to elevated HR frequencies and hypersensitivity to genotoxic agents. Through complementation studies, we were now able to demonstrate that the N-terminal region and the helicase activity of RECQ4A are both essential for the cellular response to replicative stress induced by methyl methanesulfonate and cisplatin. In contrast, loss of helicase activity or deletion of the N-terminus only partially complemented the mutant hyper-recombination phenotype. Furthermore, the helicase-deficient protein lacking its N-terminus did not complement the hyper-recombination phenotype at all. Therefore, RECQ4A seems to possess at least two different and independent sub-functions involved in the suppression of HR. By in vitro analysis, we showed that the helicase core was able to regress an artificial replication fork. Swapping of the terminal regions of RECQ4A with the closely related but functionally distinct helicase RECQ4B indicated that in contrast to the C-terminus, the N-terminus of RECQ4A was required for its specific functions in DNA repair and recombination.
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Affiliation(s)
- Susan Schröpfer
- Botanical Institute II, Karlsruhe Institute of Technology, Hertzstrasse 16, Karlsruhe 76187, Germany and Institute for Biosafety in Plant Biotechnology, Julius Kühn Institute (JKI), Erwin-Baur-Strasse 27, Quedlinburg 06484, Germany
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