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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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Zaragoza JZ, Klap K, Heidstra R, Zhou W, Scheres B. The dual role of the RETINOBLASTOMA-RELATED protein in the DNA damage response is coordinated by the interaction with LXCXE-containing proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1194-1206. [PMID: 38321589 DOI: 10.1111/tpj.16665] [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: 02/08/2022] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Living organisms possess mechanisms to safeguard genome integrity. To avoid spreading mutations, DNA lesions are detected and cell division is temporarily arrested to allow repair mechanisms. Afterward, cells either resume division or respond to unsuccessful repair by undergoing programmed cell death (PCD). How the success rate of DNA repair connects to later cell fate decisions remains incompletely known, particularly in plants. The Arabidopsis thaliana RETINOBLASTOMA-RELATED1 (RBR) protein and its partner E2FA, play both structural and transcriptional functions in the DNA damage response (DDR). Here we provide evidence that distinct RBR protein interactions with LXCXE motif-containing proteins guide these processes. Using the N849F substitution in the RBR B-pocket domain, which specifically disrupts binding to the LXCXE motif, we show that these interactions are dispensable in unchallenging conditions. However, N849F substitution abolishes RBR nuclear foci and promotes PCD and growth arrest upon genotoxic stress. NAC044, which promotes growth arrest and PCD, accumulates after the initial recruitment of RBR to foci and can bind non-focalized RBR through the LXCXE motif in a phosphorylation-independent manner, allowing interaction at different cell cycle phases. Disrupting NAC044-RBR interaction impairs PCD, but their genetic interaction points to opposite independent roles in the regulation of PCD. The LXCXE-binding dependency of the roles of RBR in the DDR suggests a coordinating mechanism to translate DNA repair success to cell survival. We propose that RBR and NAC044 act in two distinct DDR pathways, but interact to integrate input from both DDR pathways to decide upon an irreversible cell fate decision.
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Affiliation(s)
- Jorge Zamora Zaragoza
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Department of Biotechnology, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, 4793 RS, Fijnaart, The Netherlands
| | - Katinka Klap
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Renze Heidstra
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Wenkun Zhou
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ben Scheres
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Department of Biotechnology, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, 4793 RS, Fijnaart, The Netherlands
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3
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Waterworth W, Balobaid A, West C. Seed longevity and genome damage. Biosci Rep 2024; 44:BSR20230809. [PMID: 38324350 PMCID: PMC11111285 DOI: 10.1042/bsr20230809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/08/2024] Open
Abstract
Seeds are the mode of propagation for most plant species and form the basis of both agriculture and ecosystems. Desiccation tolerant seeds, representative of most crop species, can survive maturation drying to become metabolically quiescent. The desiccated state prolongs embryo viability and provides protection from adverse environmental conditions, including seasonal periods of drought and freezing often encountered in temperate regions. However, the capacity of the seed to germinate declines over time and culminates in the loss of seed viability. The relationship between environmental conditions (temperature and humidity) and the rate of seed deterioration (ageing) is well defined, but less is known about the biochemical and genetic factors that determine seed longevity. This review will highlight recent advances in our knowledge that provide insight into the cellular stresses and protective mechanisms that promote seed survival, with a focus on the roles of DNA repair and response mechanisms. Collectively, these pathways function to maintain the germination potential of seeds. Understanding the molecular basis of seed longevity provides important new genetic targets for the production of crops with enhanced resilience to changing climates and knowledge important for the preservation of plant germplasm in seedbanks.
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Affiliation(s)
- Wanda Waterworth
- Centre for Plant Sciences, University of Leeds, Woodhouse Lane, Leeds LS2
9JT, U.K
| | - Atheer Balobaid
- Centre for Plant Sciences, University of Leeds, Woodhouse Lane, Leeds LS2
9JT, U.K
| | - Chris West
- Centre for Plant Sciences, University of Leeds, Woodhouse Lane, Leeds LS2
9JT, U.K
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4
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Braat J, Havaux M. The SIAMESE family of cell-cycle inhibitors in the response of plants to environmental stresses. FRONTIERS IN PLANT SCIENCE 2024; 15:1362460. [PMID: 38434440 PMCID: PMC10904545 DOI: 10.3389/fpls.2024.1362460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
Environmental abiotic constraints are known to reduce plant growth. This effect is largely due to the inhibition of cell division in the leaf and root meristems caused by perturbations of the cell cycle machinery. Progression of the cell cycle is regulated by CDK kinases whose phosphorylation activities are dependent on cyclin proteins. Recent results have emphasized the role of inhibitors of the cyclin-CDK complexes in the impairment of the cell cycle and the resulting growth inhibition under environmental constraints. Those cyclin-CDK inhibitors (CKIs) include the KRP and SIAMESE families of proteins. This review presents the current knowledge on how CKIs respond to environmental changes and on the role played by one subclass of CKIs, the SIAMESE RELATED proteins (SMRs), in the tolerance of plants to abiotic stresses. The SMRs could play a central role in adjusting the balance between growth and stress defenses in plants exposed to environmental stresses.
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Affiliation(s)
| | - Michel Havaux
- Aix Marseille University, CEA, CNRS UMR7265, Bioscience and Biotechnology Institute of Aix Marseille, Saint-Paul-lez-Durance, France
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5
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Vladejić J, Kovacik M, Zwyrtková J, Szurman-Zubrzycka M, Doležel J, Pecinka A. Zeocin-induced DNA damage response in barley and its dependence on ATR. Sci Rep 2024; 14:3119. [PMID: 38326519 PMCID: PMC10850495 DOI: 10.1038/s41598-024-53264-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/30/2024] [Indexed: 02/09/2024] Open
Abstract
DNA damage response (DDR) is an essential mechanism by which living organisms maintain their genomic stability. In plants, DDR is important also for normal growth and yield. Here, we explored the DDR of a temperate model crop barley (Hordeum vulgare) at the phenotypic, physiological, and transcriptomic levels. By a series of in vitro DNA damage assays using the DNA strand break (DNA-SB) inducing agent zeocin, we showed reduced root growth and expansion of the differentiated zone to the root tip. Genome-wide transcriptional profiling of barley wild-type and plants mutated in DDR signaling kinase ATAXIA TELANGIECTASIA MUTATED AND RAD3-RELATED (hvatr.g) revealed zeocin-dependent, ATR-dependent, and zeocin-dependent/ATR-independent transcriptional responses. Transcriptional changes were scored also using the newly developed catalog of 421 barley DDR genes with the phylogenetically-resolved relationships of barley SUPRESSOR OF GAMMA 1 (SOG1) and SOG1-LIKE (SGL) genes. Zeocin caused up-regulation of specific DDR factors and down-regulation of cell cycle and histone genes, mostly in an ATR-independent manner. The ATR dependency was obvious for some factors associated with DDR during DNA replication and for many genes without an obvious connection to DDR. This provided molecular insight into the response to DNA-SB induction in the large and complex barley genome.
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Affiliation(s)
- Jovanka Vladejić
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Martin Kovacik
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jana Zwyrtková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia.
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6
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Zhang B, Deng C, Wang S, Deng Q, Chu Y, Bai Z, Huang A, Zhang Q, He Q. The RNA landscape of Dunaliella salina in response to short-term salt stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1278954. [PMID: 38111875 PMCID: PMC10726701 DOI: 10.3389/fpls.2023.1278954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/10/2023] [Indexed: 12/20/2023]
Abstract
Using the halotolerant green microalgae Dunaliella salina as a model organism has special merits, such as a wide range of salt tolerance, unicellular organism, and simple life cycle and growth conditions. These unique characteristics make it suitable for salt stress study. In order to provide an overview of the response of Dunaliella salina to salt stress and hopefully to reveal evolutionarily conserved mechanisms of photosynthetic organisms in response to salt stress, the transcriptomes and the genome of the algae were sequenced by the second and the third-generation sequencing technologies, then the transcriptomes under salt stress were compared to the transcriptomes under non-salt stress with the newly sequenced genome as the reference genome. The major cellular biological processes that being regulated in response to salt stress, include transcription, protein synthesis, protein degradation, protein folding, protein modification, protein transport, cellular component organization, cell redox homeostasis, DNA repair, glycerol synthesis, energy metabolism, lipid metabolism, and ion homeostasis. This study gives a comprehensive overview of how Dunaliella salina responses to salt stress at transcriptomic level, especially characterized by the nearly ubiquitous up-regulation of the genes involving in protein folding, DNA repair, and cell redox homeostasis, which may confer the algae important mechanisms to survive under salt stress. The three fundamental biological processes, which face huge challenges under salt stress, are ignored by most scientists and are worth further deep study to provide useful information for breeding economic important plants competent in tolerating salt stress, other than only depending on the commonly acknowledged osmotic balance and ion homeostasis.
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Affiliation(s)
- Bingbing Zhang
- The Research Institute of Qinghai-Tibet Plateau, Southwest Minzu University, Chengdu, China
| | - Caiyun Deng
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Shuo Wang
- The Research Institute of Qinghai-Tibet Plateau, Southwest Minzu University, Chengdu, China
| | - Qianyi Deng
- The Research Institute of Qinghai-Tibet Plateau, Southwest Minzu University, Chengdu, China
| | - Yongfan Chu
- Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, China
| | - Ziwei Bai
- Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, China
| | - Axiu Huang
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Qinglian Zhang
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Qinghua He
- Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, China
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7
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Ye C, Guo J, Zhou XQ, Chen DG, Liu J, Peng X, Jaremko M, Jaremko Ł, Guo T, Liu CG, Chen K. The Dsup coordinates grain development and abiotic stress in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108184. [PMID: 37977025 DOI: 10.1016/j.plaphy.2023.108184] [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: 07/06/2023] [Revised: 10/06/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
DNA damage is a serious threat to all living organisms and may be induced by environmental stressors. Previous studies have revealed that the tardigrade (Ramazzotius varieornatus) DNA damage suppressor protein Dsup has protective effects in human cells and tobacco. However, whether Dsup provides radiation damage protection more widely in crops is unclear. To explore the effects of Dsup in other crops, stable Dsup overexpression lines through Agrobacterium-mediated transformation were generated and their agronomic traits were deeply investigated. In this study, the overexpression of Dsup not only enhanced the DNA damage resistance at the seeds and seedlings stages, they also exhibited grain size enlargement and starch granule structure and cell size alteration by the scanning electron microscopy observation. Notably, the RNA-seq revealed that the Dsup plants increased radiation-related and abiotic stress-related gene expression in comparison to wild types, suggesting that Dsup is capable to coordinate normal growth and abiotic stress resistance in rice. Immunoprecipitation enrichment with liquid chromatography-tandem mass spectrometry (IP-LC-MS) assays uncovered 21 proteins preferably interacting with Dsup in plants, suggesting that Dsup binds to transcription and translation related proteins to regulate the homeostasis between DNA protection and plant development. In conclusion, our data provide a detailed agronomic analysis of Dsup plants and potential mechanisms of Dsup function in crops. Our findings provide novel insights for the breeding of crop radiation resistance.
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Affiliation(s)
- Chanjuan Ye
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Jie Guo
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Xin-Qiao Zhou
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Da-Gang Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Juan Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Xin Peng
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Łukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Tao Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chuan-Guang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China.
| | - Ke Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetic and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agricultural and Rural Affairs, Guangzhou, 510640, China.
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8
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Kitavi M, Gemenet DC, Wood JC, Hamilton JP, Wu S, Fei Z, Khan A, Buell CR. Identification of genes associated with abiotic stress tolerance in sweetpotato using weighted gene co-expression network analysis. PLANT DIRECT 2023; 7:e532. [PMID: 37794882 PMCID: PMC10546384 DOI: 10.1002/pld3.532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/22/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
Sweetpotato, Ipomoea batatas (L.), a key food security crop, is negatively impacted by heat, drought, and salinity stress. The orange-fleshed sweetpotato cultivar "Beauregard" was exposed to heat, salt, and drought treatments for 24 and 48 h to identify genes responding to each stress condition in leaves. Analysis revealed both common (35 up regulated, 259 down regulated genes in the three stress conditions) and unique sets of up regulated (1337 genes by drought, 516 genes by heat, and 97 genes by salt stress) and down regulated (2445 genes by drought, 678 genes by heat, and 204 genes by salt stress) differentially expressed genes (DEGs) suggesting common, yet stress-specific transcriptional responses to these three abiotic stressors. Gene Ontology analysis of down regulated DEGs common to both heat and salt stress revealed enrichment of terms associated with "cell population proliferation" suggestive of an impact on the cell cycle by the two stress conditions. To identify shared and unique gene co-expression networks under multiple abiotic stress conditions, weighted gene co-expression network analysis was performed using gene expression profiles from heat, salt, and drought stress treated 'Beauregard' leaves yielding 18 co-expression modules. One module was enriched for "response to water deprivation," "response to abscisic acid," and "nitrate transport" indicating synergetic crosstalk between nitrogen, water, and phytohormones with genes encoding osmotin, cell expansion, and cell wall modification proteins present as key hub genes in this drought-associated module. This research lays the groundwork for exploring to a further degree, mechanisms for abiotic stress tolerance in sweetpotato.
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Affiliation(s)
- Mercy Kitavi
- Research Technology Support Facility (RTSF)Michigan State UniversityEast LansingMichiganUSA
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
| | - Dorcus C. Gemenet
- International Potato CenterLimaPeru
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF HouseNairobiKenya
| | - Joshua C. Wood
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
| | - John P. Hamilton
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
- Department of Crop & Soil SciencesUniversity of GeorgiaAthensGeorgiaUSA
| | - Shan Wu
- Boyce Thompson InstituteCornell UniversityIthacaNew YorkUSA
| | - Zhangjun Fei
- Boyce Thompson InstituteCornell UniversityIthacaNew YorkUSA
| | - Awais Khan
- International Potato CenterLimaPeru
- Present address:
Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant ScienceCornell UniversityGenevaNew YorkUSA
| | - C. Robin Buell
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
- Department of Crop & Soil SciencesUniversity of GeorgiaAthensGeorgiaUSA
- Institute of Plant Breeding, Genetics, & GenomicsUniversity of GeorgiaAthensGeorgiaUSA
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9
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Banerjee G, Singh D, Pandey C, Jonwal S, Basu U, Parida SK, Pandey A, Sinha AK. Rice Mitogen-Activated Protein Kinase regulates serotonin accumulation and interacts with cell cycle regulators under prolonged UV-B exposure. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108078. [PMID: 37832368 DOI: 10.1016/j.plaphy.2023.108078] [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: 03/17/2023] [Revised: 09/12/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023]
Abstract
Stress conditions such as UV-B exposure activates MAPKs in Arabidopsis and rice. UV-B radiation is hazardous to plant as it causes photosystem disruption, DNA damage and ROS generation. Here we report its effect on biological pathways by studying the global changes in transcript profile in rice seedling exposed to UV-B radiation for 1 h and 16 h. Short UV-B exposure (1 h) led to moderate changes, while a drastic change in transcript landscape was observed after long term UV-B exposure (16 h) in rice seedlings. Prolonged UV-B exposure negatively impacts the expression of cell cycle regulating genes and several other metabolic pathways in developing seedlings. MAP kinase signaling cascade gets activated upon UV-B exposure similar to reports in Arabidopsis indicating conservation of its function in both dicot and monocot. Expression analysis in inducible overexpression transgenic lines of MPK3 and MPK6 shows higher transcript abundance of phytoalexin biosynthesis gene like Oryzalexin D synthase and Momilactone A synthase, along with serotonin biosynthesis genes. An accumulation of serotonin was observed upon UV-B exposure and its abundance positively correlates with the MPK3 and MPK6 transcript level in the respective over-expression lines. Interestingly, multiple cell cycle inhibitor proteins including WEE1 and SMR1 interact with MPK3 and MPK6 thus, implying a major role of this pathway in cell cycle regulation under stress condition. Overall overexpression of MPK3 and MPK6 found to be detrimental for rice as overexpression lines shows higher cell death and compromised tolerance to UV-B.
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Affiliation(s)
- Gopal Banerjee
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Dhanraj Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Chandana Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Sarvesh Jonwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Udita Basu
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
| | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India.
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10
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Sears RG, Rigoulot SB, Occhialini A, Morgan B, Kakeshpour T, Brabazon H, Barnes CN, Seaberry EM, Jacobs B, Brown C, Yang Y, Schimel TM, Lenaghan SC, Neal Stewart C. Engineered gamma radiation phytosensors for environmental monitoring. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1745-1756. [PMID: 37224108 PMCID: PMC10440981 DOI: 10.1111/pbi.14072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/13/2023] [Accepted: 04/24/2023] [Indexed: 05/26/2023]
Abstract
Nuclear energy, already a practical solution for supplying energy on a scale similar to fossil fuels, will likely increase its footprint over the next several decades to meet current climate goals. Gamma radiation is produced during fission in existing nuclear reactors and thus the need to detect leakage from nuclear plants, and effects of such leakage on ecosystems will likely also increase. At present, gamma radiation is detected using mechanical sensors that have several drawbacks, including: (i) limited availability; (ii) reliance on power supply; and (iii) requirement of human presence in dangerous areas. To overcome these limitations, we have developed a plant biosensor (phytosensor) to detect low-dose ionizing radiation. The system utilizes synthetic biology to engineer a dosimetric switch into potato utilizing the plant's native DNA damage response (DDR) machinery to produce a fluorescent output. In this work, the radiation phytosensor was shown to respond to a wide range of gamma radiation exposure (10-80 Grey) producing a reporter signal that was detectable at >3 m. Further, a pressure test of the top radiation phytosensor in a complex mesocosm demonstrated full function of the system in a 'real world' scenario.
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Affiliation(s)
- Robert G. Sears
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Stephen B. Rigoulot
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Alessandro Occhialini
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
- Department of Food ScienceThe University of TennesseeKnoxvilleTennesseeUSA
| | - Britany Morgan
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Tayebeh Kakeshpour
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Holly Brabazon
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Caitlin N. Barnes
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Erin M. Seaberry
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Brianna Jacobs
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Chandler Brown
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Yongil Yang
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Tayler M. Schimel
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
- Department of Food ScienceThe University of TennesseeKnoxvilleTennesseeUSA
| | - Scott C. Lenaghan
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
- Department of Food ScienceThe University of TennesseeKnoxvilleTennesseeUSA
| | - C. Neal Stewart
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
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11
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Chen H, Pan T, Zheng X, Huang Y, Wu C, Yang T, Gao S, Wang L, Yan S. The ATR-WEE1 kinase module promotes SUPPRESSOR OF GAMMA RESPONSE 1 translation to activate replication stress responses. THE PLANT CELL 2023; 35:3021-3034. [PMID: 37159556 PMCID: PMC10396359 DOI: 10.1093/plcell/koad126] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/11/2023]
Abstract
DNA replication stress threatens genome stability and is a hallmark of cancer in humans. The evolutionarily conserved kinases ATR (ATM and RAD3-related) and WEE1 are essential for the activation of replication stress responses. Translational control is an important mechanism that regulates gene expression, but its role in replication stress responses is largely unknown. Here we show that ATR-WEE1 control the translation of SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a master transcription factor required for replication stress responses in Arabidopsis thaliana. Through genetic screening, we found that the loss of GENERAL CONTROL NONDEREPRESSIBLE 20 (GCN20) or GCN1, which function together to inhibit protein translation, suppressed the hypersensitivity of the atr or wee1 mutant to replication stress. Biochemically, WEE1 inhibits GCN20 by phosphorylating it; phosphorylated GCN20 is subsequently polyubiquitinated and degraded. Ribosome profiling experiments revealed that that loss of GCN20 enhanced the translation efficiency of SOG1, while overexpressing GCN20 had the opposite effect. The loss of SOG1 reduced the resistance of wee1 gcn20 to replication stress, whereas overexpressing SOG1 enhanced the resistance to atr or wee1 to replication stress. These results suggest that ATR-WEE1 inhibits GCN20-GCN1 activity to promote the translation of SOG1 during replication stress. These findings link translational control to replication stress responses in Arabidopsis.
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Affiliation(s)
- Hanchen Chen
- Hubei Hongshan Laboratory, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Ting Pan
- Hubei Hongshan Laboratory, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xueao Zheng
- Hubei Hongshan Laboratory, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yongchi Huang
- Hubei Hongshan Laboratory, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Chong Wu
- Hubei Hongshan Laboratory, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Tongbin Yang
- Hubei Hongshan Laboratory, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shan Gao
- Hubei Hongshan Laboratory, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Lili Wang
- Hubei Hongshan Laboratory, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shunping Yan
- Hubei Hongshan Laboratory, Wuhan 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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12
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Guo T, Liu M, Chen L, Liu Y, Li L, Li Y, Cao X, Mao Z, Wang W, Yang HQ. Photoexcited cryptochromes interact with ADA2b and SMC5 to promote the repair of DNA double-strand breaks in Arabidopsis. NATURE PLANTS 2023; 9:1280-1290. [PMID: 37488265 DOI: 10.1038/s41477-023-01461-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
Abstract
Cryptochromes (CRYs) act as blue-light photoreceptors that regulate development and circadian rhythms in plants and animals and as navigating magnetoreceptors in migratory birds. DNA double-strand breaks (DSBs) are the most serious type of DNA damage and threaten genome stability in all organisms. Although CRYs have been shown to respond to DNA damage, whether and how they participate in DSB repair is not well understood. Here we report that Arabidopsis CRYs promote the repair of DSBs through direct interactions with ADA2b and SMC5 in a blue-light-dependent manner to enhance their interaction. Mutations in CRYs and in ADA2b lead to similar enhanced DNA damage accumulation. In response to DNA damage, CRYs are localized at DSBs, and the recruitment of SMC5 to DSBs is dependent on CRYs. These results suggest that CRY-enhanced ADA2b-SMC5 interaction promotes ADA2b-mediated recruitment of SMC5 to DSBs, leading to DSB repair.
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Affiliation(s)
- Tongtong Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Minqing Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Li Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yao Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Ling Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yupeng Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoli Cao
- School of Life Sciences, Fudan University, Shanghai, China
| | - Zhilei Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wenxiu Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hong-Quan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.
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13
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Bao W, Zhang W, Huang Y, Zhao Y, Wu C, Duan L, Wang L, Yan S. Protein kinase ATR inhibits E3 ubiquitin ligase CRL4 PRL1 to stabilize ribonucleotide reductase in response to replication stress. Cell Rep 2023; 42:112685. [PMID: 37354461 DOI: 10.1016/j.celrep.2023.112685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/14/2023] [Accepted: 06/07/2023] [Indexed: 06/26/2023] Open
Abstract
The protein kinase ATR is essential for replication stress responses in all eukaryotes. Ribonucleotide reductase (RNR) catalyzes the formation of deoxyribonucleotide (dNTP), the universal building block for DNA replication and repair. However, the relationship between ATR and RNR is not well understood. Here, we show that ATR promotes the protein stability of RNR in Arabidopsis. Through an activation tagging-based genetic screen, we found that overexpression of TSO2, a small subunit of RNR, partially suppresses the hypersensitivity of the atr mutant to replication stress. Biochemically, TSO2 interacts with PRL1, a central subunit of the Cullin4-based E3 ubiquitin ligase CRL4PRL1, which polyubiquitinates TSO2 and promotes its degradation. ATR inhibits CRL4PRL1 to attenuate TSO2 degradation. Our work provides an important insight into the replication stress responses and a post-translational regulatory mechanism for RNR. Given the evolutionary conservation of the proteins involved, the ATR-PRL1-RNR module may act across eukaryotes.
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Affiliation(s)
- Weiyi Bao
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Weijia Zhang
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yongchi Huang
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yan Zhao
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Cong Wu
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Leilei Duan
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Lili Wang
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
| | - Shunping Yan
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
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14
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Yu H, Ma L, Zhao Y, Naren G, Wu H, Sun Y, Wu L, Zhang L. Characterization of nuclear DNA diversity in an individual Leymus chinensis. FRONTIERS IN PLANT SCIENCE 2023; 14:1157145. [PMID: 37346123 PMCID: PMC10280068 DOI: 10.3389/fpls.2023.1157145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/13/2023] [Indexed: 06/23/2023]
Abstract
Intraorganismal genetic heterogeneity (IGH) exists when an individual organism harbors more than one genotype among its cells. In general, intercellular DNA diversity occurs at a very low frequency and cannot be directly detected by DNA sequencing from bulk tissue. In this study, based on Sanger and high-throughput sequencing, different species, different organs, different DNA segments and a single cell were employed to characterize nucleotide mutations in Leymus chinensis. The results demonstrated that 1) the nuclear DNA showed excessive genetic heterogeneity among cells of an individual leaf or seed but the chloroplast genes remained consistent; 2) a high density of SNPs was found in the variants of the unique DNA sequence, and the similar SNP profile shared between the leaf and seed suggested that nucleotide mutation followed a certain rule and was not random; and 3) the mutation rate decreased from the genomic DNA sequence to the corresponding protein sequence. Our results suggested that Leymus chinensis seemed to consist of a collection of cells with different genetic backgrounds.
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15
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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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16
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Yu C, Hou L, Huang Y, Cui X, Xu S, Wang L, Yan S. The multi-BRCT domain protein DDRM2 promotes the recruitment of RAD51 to DNA damage sites to facilitate homologous recombination. THE NEW PHYTOLOGIST 2023; 238:1073-1084. [PMID: 36727295 DOI: 10.1111/nph.18787] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
DNA double-strand breaks (DSBs) are the most toxic form of DNA damage in cells. Homologous recombination (HR) is an error-free repair mechanism for DSBs as well as a basis for gene targeting using genome-editing techniques. Despite the importance of HR, the HR mechanism in plants is poorly understood. Through genetic screens for DNA damage response mutants (DDRMs), we find that the Arabidopsis ddrm2 mutant is hypersensitive to DSB-inducing reagents. DDRM2 encodes a protein with four BRCA1 C-terminal (BRCT) domains and is highly conserved in plants including bryophytes, the earliest land plant lineage. The plant-specific transcription factor SOG1 binds to the promoter of DDRM2 and activates its expression. In consistence, the expression of DDRM2 is induced by DSBs in a SOG1-dependent manner. In support, genetic analysis suggests that DDRM2 functions downstream of SOG1. Similar to the sog1 mutant, the ddrm2 mutant shows dramatically reduced HR efficiency. Mechanistically, DDRM2 interacts with the core HR protein RAD51 and is required for the recruitment of RAD51 to DSB sites. Our study reveals that SOG1-DDRM2-RAD51 is a novel module for HR, providing a potential target for improving the efficiency of gene targeting.
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Affiliation(s)
- Chen Yu
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Longhui Hou
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yongchi Huang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiaoyu Cui
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Shijun Xu
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Lili Wang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Shunping Yan
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
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17
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Li C, Guo Y, Wang L, Yan S. The SMC5/6 complex recruits the PAF1 complex to facilitate DNA double-strand break repair in Arabidopsis. EMBO J 2023; 42:e112756. [PMID: 36815434 PMCID: PMC10068331 DOI: 10.15252/embj.2022112756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/24/2023] Open
Abstract
DNA double-strand breaks (DSBs) are one of the most toxic forms of DNA damage, which threatens genome stability. Homologous recombination is an error-free DSB repair pathway, in which the evolutionarily conserved SMC5/6 complex (SMC5/6) plays essential roles. The PAF1 complex (PAF1C) is well known to regulate transcription. Here we show that SMC5/6 recruits PAF1C to facilitate DSB repair in plants. In a genetic screen for DNA damage response mutants (DDRMs), we found that the Arabidopsis ddrm4 mutant is hypersensitive to DSB-inducing agents and is defective in homologous recombination. DDRM4 encodes PAF1, a core subunit of PAF1C. Further biochemical and genetic studies reveal that SMC5/6 recruits PAF1C to DSB sites, where PAF1C further recruits the E2 ubiquitin-conjugating enzymes UBC1/2, which interact with the E3 ubiquitin ligases HUB1/2 to mediate the monoubiquitination of histone H2B at DSBs. These results implicate SMC5/6-PAF1C-UBC1/2-HUB1/2 as a new axis for DSB repair through homologous recombination, revealing a new mechanism of SMC5/6 and uncovering a novel function of PAF1C.
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Affiliation(s)
- Cunliang Li
- Hubei Hongshan LaboratoryWuhanChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityShenzhenChina
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureShenzhenChina
- Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Yuyu Guo
- Hubei Hongshan LaboratoryWuhanChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityShenzhenChina
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureShenzhenChina
- Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Lili Wang
- Hubei Hongshan LaboratoryWuhanChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityShenzhenChina
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureShenzhenChina
- Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Shunping Yan
- Hubei Hongshan LaboratoryWuhanChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityShenzhenChina
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureShenzhenChina
- Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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18
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Guo Z, Wang X, Li Y, Xing A, Wu C, Li D, Wang C, de Bures A, Zhang Y, Guo S, Sáez-Vasquez J, Shen Z, Hu Z. Arabidopsis SMO2 modulates ribosome biogenesis by maintaining the RID2 abundance during organ growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:96-109. [PMID: 36705084 DOI: 10.1111/tpj.16121] [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: 06/03/2022] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Ribosome biogenesis is a process of making ribosomes that is tightly linked with plant growth and development. Here, through a suppressor screen for the smo2 mutant, we found that lack of a ribosomal stress response mediator, ANAC082 partially restored growth defects of the smo2 mutant, indicating SMO2 is required for the repression of nucleolar stress. Consistently, the smo2 knock-out mutant exhibited typical phenotypes characteristic of ribosome biogenesis mutants, such as pointed leaves, aberrant leaf venation, disrupted nucleolar structure, abnormal distribution of rRNA precursors, and enhanced tolerance to aminoglycoside antibiotics that target ribosomes. SMO2 interacted with ROOT INITIATION DEFECTIVE 2 (RID2), a methyltransferase-like protein required for pre-rRNA processing. SMO2 enhanced RID2 solubility in Escherichia coli and the loss of function of SMO2 in plant cells reduced RID2 abundance, which may result in abnormal accumulation of FIBRILLARIN 1 (FIB1) and NOP56, two key nucleolar proteins, in high-molecular-weight protein complex. Taken together, our results characterized a novel plant ribosome biogenesis factor, SMO2 that maintains the abundance of RID2, thereby sustaining ribosome biogenesis during plant organ growth.
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Affiliation(s)
- Zhengfei Guo
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Xiaoyu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Yan Li
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Aiming Xing
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Chengyun Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| | - Daojun Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Chunfei Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Anne de Bures
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Universite Perpignan Via Domitia, 66860, Perpignan, Unité Mixte de Recherche 5096, France
| | - Yonghong Zhang
- Laboratory of Medicinal Plant, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, School of Basic Medicine, Hubei University of Medicine, 442000, Shiyan, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| | - Julio Sáez-Vasquez
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Universite Perpignan Via Domitia, 66860, Perpignan, Unité Mixte de Recherche 5096, France
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
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19
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Ofoe R, Thomas RH, Asiedu SK, Wang-Pruski G, Fofana B, Abbey L. Aluminum in plant: Benefits, toxicity and tolerance mechanisms. FRONTIERS IN PLANT SCIENCE 2023; 13:1085998. [PMID: 36714730 PMCID: PMC9880555 DOI: 10.3389/fpls.2022.1085998] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Aluminum (Al) is the third most ubiquitous metal in the earth's crust. A decrease in soil pH below 5 increases its solubility and availability. However, its impact on plants depends largely on concentration, exposure time, plant species, developmental age, and growing conditions. Although Al can be beneficial to plants by stimulating growth and mitigating biotic and abiotic stresses, it remains unknown how Al mediates these effects since its biological significance in cellular systems is still unidentified. Al is considered a major limiting factor restricting plant growth and productivity in acidic soils. It instigates a series of phytotoxic symptoms in several Al-sensitive crops with inhibition of root growth and restriction of water and nutrient uptake as the obvious symptoms. This review explores advances in Al benefits, toxicity and tolerance mechanisms employed by plants on acidic soils. These insights will provide directions and future prospects for potential crop improvement.
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Affiliation(s)
- Raphael Ofoe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
| | - Raymond H. Thomas
- School of Science and the Environment, Memorial University of Newfoundland, Grenfell Campus, Corner Brook, NL, Canada
| | - Samuel K. Asiedu
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
| | - Gefu Wang-Pruski
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
| | - Bourlaye Fofana
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - Lord Abbey
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
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20
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Meng X, Wang Q, Hao R, Li X, Li M, Hu R, Du H, Hu Z, Yu B, Li S. RNA-binding protein MAC5A interacts with the 26S proteasome to regulate DNA damage response in Arabidopsis. PLANT PHYSIOLOGY 2023; 191:446-462. [PMID: 36331331 PMCID: PMC9806599 DOI: 10.1093/plphys/kiac510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
DNA damage response (DDR) in eukaryotes is essential for the maintenance of genome integrity in challenging environments. The regulatory mechanisms of DDR have been well-established in yeast and humans. However, increasing evidence supports the idea that plants seem to employ different signaling pathways that remain largely unknown. Here, we report the role of MODIFIER OF SNC1, 4-ASSOCIATED COMPLEX SUBUNIT 5A (MAC5A) in DDR in Arabidopsis (Arabidopsis thaliana). Lack of MAC5A in mac5a mutants causes hypersensitive phenotypes to methyl methanesulfonate (MMS), a DNA damage inducer. Consistent with this observation, MAC5A can regulate alternative splicing of DDR genes to maintain the proper response to genotoxic stress. Interestingly, MAC5A interacts with the 26S proteasome (26SP) and is required for its proteasome activity. MAC core subunits are also involved in MMS-induced DDR. Moreover, we find that MAC5A, the MAC core subunits, and 26SP may act collaboratively to mediate high-boron-induced growth repression through DDR. Collectively, our findings uncover the crucial role of MAC in MMS-induced DDR in orchestrating growth and stress adaptation in plants.
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Affiliation(s)
- Xiangxiang Meng
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Quanhui Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Ruili Hao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Xudong Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mu Li
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666, USA
| | - Ruibo Hu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, College of Agriculture, Henan University, Kaifeng 475004, China
| | - Bin Yu
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0666, USA
| | - Shengjun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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21
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Singh S, Chaudhary R, Deshmukh R, Tiwari S. Opportunities and challenges with CRISPR-Cas mediated homologous recombination based precise editing in plants and animals. PLANT MOLECULAR BIOLOGY 2023; 111:1-20. [PMID: 36315306 DOI: 10.1007/s11103-022-01321-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
We summarise recent advancements to achieve higher homologous recombination based gene targeting efficiency in different animals and plants. The genome editing has revolutionized the agriculture and human therapeutic sectors by its ability to create precise, stable and predictable mutations in the genome. It depends upon targeted double-strand breaks induction by the engineered endonucleases, which then gets repaired by highly conserved endogenous DNA repair mechanisms. The repairing could be done either through non-homologous end joining (NHEJ) or homology-directed repair (HDR) pathways. The HDR-based editing can be applied for precise gene targeting such as insertion of a new gene, gene replacement and altering of the regulatory sequence of a gene to control the existing protein expression. However, HDR-mediated editing is considered challenging because of lower efficiency in higher eukaryotes, thus, preventing its widespread application. This article reviews the recent progress of HDR-mediated editing and discusses novel strategies such as cell cycle synchronization, modulation of DNA damage repair factors, engineering of Cas protein favoring HDR and CRISPR-Cas reagents delivery methods to improve efficiency for generating knock-in events in both plants and animals. Further, multiplexing of described methods may be promising towards achieving higher donor template-assisted homologous recombination efficiency at the target locus.
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Affiliation(s)
- Surender Singh
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India
- Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Roni Chaudhary
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India
- Regional Centre for Biotechnology, Faridabad, 121001, India
| | | | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India.
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22
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Wang J, Moeen-ud-din M, Yin R, Yang S. ROS Homeostasis Involved in Dose-Dependent Responses of Arabidopsis Seedlings to Copper Toxicity. Genes (Basel) 2022; 14:11. [PMID: 36672752 PMCID: PMC9858908 DOI: 10.3390/genes14010011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/13/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
As an essential element in plant nutrition, copper (Cu) can promote or inhibit plant growth depending on its concentration. However, the dose-dependent effects of copper, particularly on DNA damage associated with reactive oxygen species (ROS) homeostasis, are much less understood. In this work, we analyzed the dual effect of Cu (5, 20, and 60 μM) on the reproductive performance of Arabidopsis plants. Whereas Cu5 promoted inflorescence initiation and increased kilo seed weight, two higher concentrations, Cu20 and Cu60, delayed inflorescence initiation and negatively affected silique size. Excess Cu also induced changes in cellular redox homeostasis, which was examined by in situ visualization and measurements of ROS, including superoxide (O2•-), hydrogen peroxide (H2O2), malonyldialdehyde (MDA), and plasma membrane damage. The most dramatic increases in the production of O2•- and H2O2 along with increased activity of superoxide dismutase (SOD) and glutathione peroxidase (GPX) and decreased activity of catalase (CAT) and ascorbate peroxidase (APX) were observed in roots with Cu60. Oxidative stress also modulated the expression levels of a number of genes involved in the DNA damage response (DDR), particularly those related to DNA repair. The Cu-induced chlorosis of Arabidopsis seedlings could be alleviated by exogenous addition of glutathione (GSH) and ascorbate (Asc), as the chlorophyll content was significantly increased. Overall, internal homeostasis ROS and the associated DDR pathway and the corresponding scavenging mechanisms play a central role in the response of Arabidopsis to oxidative stress induced by inhibitory Cu concentrations. Our results have shown, for the first time, that the biphasic responses of Arabidopsis seedlings to increasing Cu concentrations involve different DNA damage responses and oxidative reactions. They provide the basis for elucidating the network of Cu-induced DDR-related genes and the regulatory mechanism of the complex ROS production and scavenging system.
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Affiliation(s)
| | | | | | - Shaohui Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
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23
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Jia T, Pu C, Qin T, Liu B, Yao G, Xun Z, Wang B, Tian Y, Zhang Z, Xu H, Zhao C. Azocalixarene-Based Supramolecular System for the Detection of Paraquat via an Improved Indicator Displacement Assay. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15981-15989. [PMID: 36510782 DOI: 10.1021/acs.jafc.2c06051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In view of the lethal toxicity of paraquat (PQ) on human health, herein, a simple indicator displacement assay (IDA) based on an azo-modified calixarene host (azoCX[4]) and a fluorophore guest (p-DPD) were elaborately constructed for PQ detection in environmental water samples and plant surfaces. The fluorescent signal of p-DPD in the probe can be quenched by azoCX[4] through a photon-induced electron transfer process and recovered upon the addition of PQ within 10 s. The detection range of the p-DPD@azoCX[4] probe was calculated to be 0.35-8 μM in the Tris-HCl buffer solutions (pH = 7.4). Moreover, this probe exhibited excellent detection selectivity toward PQ over five herbicides (glyphosate, bispyribac, atrazine, ametryn, and bensulfuron methyl), together with anti-interference abilities in the presence of inorganic ions (K+, Na+, Zn2+, Ni2+, Li+, F-, Cl-, Br-, CO32-, HCO3-, and NO3-) and amino acids (Asp, Arg, Glu, Ala, and Cys). Particularly, the probe was successfully used to detect PQ in real water samples with acceptable accuracy and showed potential applications for on-site detection with paper-based test strips and on the leaf surface. We believe that this simplified IDA-based probe provided an effective detecting tool for PQ, and the design strategy would guide the further development of new IDA sensing systems.
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Affiliation(s)
- Tianhao Jia
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education and State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong510642, China
| | - Chunmei Pu
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education and State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong510642, China
| | - Tianyi Qin
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education and State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong510642, China
| | - Bin Liu
- College of Material Science and Engineering, Shenzhen University, Shenzhen, Guangdong518060, China
| | - Guangkai Yao
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education and State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong510642, China
| | - Zhiqing Xun
- Guangzhou Quality Supervision and Testing Institute, 1-2 Zhujiang Road, Guangzhou, Guangdong511447, China
| | - Bingfeng Wang
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education and State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong510642, China
| | - Yongqing Tian
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education and State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong510642, China
| | - Zhixiang Zhang
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education and State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong510642, China
| | - Hanhong Xu
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education and State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong510642, China
| | - Chen Zhao
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education and State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong510642, China
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24
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Vladejić J, Yang F, Dvořák Tomaštíková E, Doležel J, Palecek JJ, Pecinka A. Analysis of BRCT5 domain-containing proteins reveals a new component of DNA damage repair in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:1023358. [PMID: 36578335 PMCID: PMC9791218 DOI: 10.3389/fpls.2022.1023358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The integrity of plant genetic information is constantly challenged by various internal and external factors. Therefore, plants use a sophisticated molecular network to identify, signal and repair damaged DNA. Here, we report on the identification and analysis of four uncharacterized Arabidopsis BRCT5 DOMAIN CONTAINING PROTEINs (BCPs). Proteins with the BRCT5 domain are frequently involved in the maintenance of genome stability across eukaryotes. The screening for sensitivity to induced DNA damage identified BCP1 as the most interesting candidate. We show that BCP1 loss of function mutants are hypersensitive to various types of DNA damage and accumulate an increased number of dead cells in root apical meristems upon DNA damage. Analysis of publicly available sog1 transcriptomic and SOG1 genome-wide DNA binding data revealed that BCP1 is inducible by gamma radiation and is a direct target of this key DNA damage signaling transcription factor. Importantly, bcp1 plants showed a reduced frequency of somatic homologous recombination in response to both endogenous and induced DNA damage. Altogether, we identified a novel plant-specific DNA repair factor that acts downstream of SOG1 in homology-based repair.
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Affiliation(s)
- Jovanka Vladejić
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czechia
| | - Fen Yang
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Eva Dvořák Tomaštíková
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czechia
| | - Jaroslav Doležel
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czechia
| | - Jan J. Palecek
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czechia
| | - Ales Pecinka
- Institute of Experimental Botany (IEB), Czech Acad Sci, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
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25
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Du J, Liu Y, Lu L, Shi J, Xu L, Li Q, Cheng X, Chen J, Zhang X. Accumulation of DNA damage alters microRNA gene transcription in Arabidopsis thaliana. BMC PLANT BIOLOGY 2022; 22:576. [PMID: 36503409 PMCID: PMC9743578 DOI: 10.1186/s12870-022-03951-9] [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: 08/18/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) and other epigenetic modifications play fundamental roles in all eukaryotic biological processes. DNA damage repair is a key process for maintaining the genomic integrity of different organisms exposed to diverse stresses. However, the reaction of miRNAs in the DNA damage repair process is unclear. RESULTS In this study, we found that the simultaneous mutation of zinc finger DNA 3'-phosphoesterase (ZDP) and AP endonuclease 2 (APE2), two genes that play overlapping roles in active DNA demethylation and base excision repair (BER), led to genome-wide alteration of miRNAs. The transcripts of newly transcribed miRNA-encoding genes (MIRs) decreased significantly in zdp/ape2, indicating that the mutation of ZDP and APE2 affected the accumulation of miRNAs at the transcriptional level. In addition, the introduction of base damage with the DNA-alkylating reagent methyl methanesulfonate (MMS) accelerated the reduction of miRNAs in zdp/ape2. Further mutation of FORMAMIDOPYRIMIDINE DNA GLYCOSYLASE (FPG), a bifunctional DNA glycosylase/lyase, rescued the accumulation of miRNAs in zdp/ape2, suggesting that the accumulation of DNA damage repair intermediates induced the transcriptional repression of miRNAs. CONCLUSIONS Our investigation indicates that the accumulation of DNA damage repair intermediates inhibit miRNAs accumulation by inhibiting MIR transcriptions.
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Affiliation(s)
- Juan Du
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianfei Shi
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Longqian Xu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Department of Life Sciences, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Qi Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofei Cheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Jinfeng Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zheng WJ, Li WQ, Peng Y, Shao Y, Tang L, Liu CT, Zhang D, Zhang LJ, Li JH, Luo WZ, Yuan ZC, Zhao BR, Mao BG. E2Fs co-participate in cadmium stress response through activation of MSHs during the cell cycle. FRONTIERS IN PLANT SCIENCE 2022; 13:1068769. [PMID: 36531377 PMCID: PMC9749859 DOI: 10.3389/fpls.2022.1068769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Cadmium is one of the most common heavy metal contaminants found in agricultural fields. MutSα, MutSβ, and MutSγ are three different MutS-associated protein heterodimer complexes consisting of MSH2/MSH6, MSH2/MSH3, and MSH2/MSH7, respectively. These complexes have different mismatch recognition properties and abilities to support MMR. However, changes in mismatch repair genes (OsMSH2, OsMSH3, OsMSH6, and OsMSH7) of the MutS system in rice, one of the most important food crops, under cadmium stress and their association with E2Fs, the key transcription factors affecting cell cycles, are poorly evaluated. In this study, we systematically categorized six rice E2Fs and confirmed that OsMSHs were the downstream target genes of E2F using dual-luciferase reporter assays. In addition, we constructed four msh mutant rice varieties (msh2, msh3, msh6, and msh7) using the CRISPR-Cas9 technology, exposed these mutant rice seedlings to different concentrations of cadmium (0, 2, and 4 mg/L) and observed changes in their phenotype and transcriptomic profiles using RNA-Seq and qRT-PCR. We found that the difference in plant height before and after cadmium stress was more significant in mutant rice seedlings than in wild-type rice seedlings. Transcriptomic profiling and qRT-PCR quantification showed that cadmium stress specifically mobilized cell cycle-related genes ATR, CDKB2;1, MAD2, CycD5;2, CDKA;1, and OsRBR1. Furthermore, we expressed OsE2Fs in yeasts and found that heterologous E2F expression in yeast strains regulated cadmium tolerance by regulating MSHs expression. Further exploration of the underlying mechanisms revealed that cadmium stress may activate the CDKA/CYCD complex, which phosphorylates RBR proteins to release E2F, to regulate downstream MSHs expression and subsequent DNA damage repairment, thereby enhancing the response to cadmium stress.
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Affiliation(s)
- Wen-Jie Zheng
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Wang-Qing Li
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Yan Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Ye Shao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Li Tang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Ci-Tao Liu
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Dan Zhang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Lan-Jing Zhang
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Ji-Huan Li
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Wu-Zhong Luo
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Zhi-Cheng Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Bing-Ran Zhao
- Longping Branch, College of Biology, Hunan University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Bi-Gang Mao
- Longping Branch, College of Biology, Hunan University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
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27
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Sun L, Xue C, Guo C, Jia C, Li X, Tai P. Regulatory actions of rare earth elements (La and Gd) on the cell cycle of root tips in rice seedlings (Oryza sativa L.). CHEMOSPHERE 2022; 307:135795. [PMID: 35917980 DOI: 10.1016/j.chemosphere.2022.135795] [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: 05/19/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
The continuous expansion of the application of rare earth elements (REEs) in various fields has attracted attention to their biosafety. At present, the molecular mechanisms underlying the biological effects of REEs are unclear. In this study, the effects of lanthanum (La) and gadolinium (Gd) on cell cycle progression in the root tips of rice seedlings were investigated. Low concentrations of REEs (0.1 mg L-1) induced an increase in the number of cells in the prophase and metaphase, while high concentrations of REEs (10 mg L-1) induced an increase in the number of cells in the late and terminal stages of the cell cycle, and apoptosis or necrosis. Additionally, low concentrations of REEs induced a significant increase in the expression of the cell cycle factors WEE1, CDKA;1, and CYCB1;1, and promoted the G2/M phase and accelerated root tip growth. However, at high REEs concentrations, the DNA damage response sensitized by BRCA1, MRE11, and TP53 could that prevent root tip growth by inhibiting the transcription factor E2F, resulting in obvious G1/S phase transition block and delayed G2/M phase conversion. Furthermore, by comparing the biological effect mechanisms of La and Gd, we found that these two REEs share regulatory actions on the cell cycle of root tips in rice seedlings.
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Affiliation(s)
- Lizong Sun
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Chenyang Xue
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China; Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Guo
- School of Environmental and Safety Engineering, Liaoning Petrochemical University, Fushun, 113001, China
| | - Chunyun Jia
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Xiaojun Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China.
| | - Peidong Tai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China.
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de Luxán-Hernández C, Lohmann J, Tranque E, Chumova J, Binarova P, Salinas J, Weingartner M. MDF is a conserved splicing factor and modulates cell division and stress response in Arabidopsis. Life Sci Alliance 2022; 6:6/1/e202201507. [PMID: 36265897 PMCID: PMC9585968 DOI: 10.26508/lsa.202201507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 02/05/2023] Open
Abstract
The coordination of cell division with stress response is essential for maintaining genome stability in plant meristems. Proteins involved in pre-mRNA splicing are important for these processes in animal and human cells. Based on its homology to the splicing factor SART1, which is implicated in the control of cell division and genome stability in human cells, we analyzed if MDF has similar functions in plants. We found that MDF associates with U4/U6.U5 tri-snRNP proteins and is essential for correct splicing of 2,037 transcripts. Loss of MDF function leads to cell division defects and cell death in meristems and was associated with up-regulation of stress-induced genes and down-regulation of mitotic regulators. In addition, the mdf-1 mutant is hypersensitive to DNA damage treatment supporting its role in coordinating stress response with cell division. Our analysis of a dephosphomutant of MDF suggested how its protein activity might be controlled. Our work uncovers the conserved function of a plant splicing factor and provides novel insight into the interplay of pre-mRNA processing and genome stability in plants.
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Affiliation(s)
| | - Julia Lohmann
- Institute of Plant Sciences and Microbiology, University of Hamburg, Hamburg, Germany
| | - Eduardo Tranque
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas “Margarita Salas” (CSIC), Madrid, Spain
| | - Jana Chumova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pavla Binarova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas “Margarita Salas” (CSIC), Madrid, Spain
| | - Magdalena Weingartner
- Institute of Plant Sciences and Microbiology, University of Hamburg, Hamburg, Germany
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29
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Garcia N, Yin L, Dukowic-Schulze S, Milsted C, Kianian PMA, Kianian S, Pawlowski WP, Chen C. Comparison of meiotic transcriptomes of three maize inbreds with different origins reveals differences in cell cycle and recombination. BMC Genomics 2022; 23:702. [PMID: 36224518 PMCID: PMC9554999 DOI: 10.1186/s12864-022-08922-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022] Open
Abstract
Background Cellular events during meiosis can differ between inbred lines in maize. Substantial differences in the average numbers of chiasmata and double-strand breaks (DSBs) per meiotic cell have been documented among diverse inbred lines of maize: CML228, a tropical maize inbred line, B73 and Mo17, temperate maize lines. To determine if gene expression might explain these observed differences, an RNA-Seq experiment was performed on CML228 male meiocytes which was compared to B73 and Mo17 male meiocytes, where plants were grown in the same controlled environment. Results We found that a few DSB-repair/meiotic genes which promote class I crossovers (COs) and the Zyp1 gene which limits newly formed class I COs were up-regulated, whereas Mus81 homolog 2 which promotes class II COs was down-regulated in CML228. Although we did not find enriched gene ontology (GO) categories directly related to meiosis, we found that GO categories in membrane, localization, proteolysis, energy processes were up-regulated in CML228, while chromatin remodeling, epigenetic regulation, and cell cycle related processes including meiosis related cell cycle processes were down-regulated in CML228. The degree of similarity in expression patterns between the three maize lines reflect their genetic relatedness: B73 and Mo17 had similar meiotic expressions and CML228 had a more distinct expression profile. Conclusions We found that meiotic related genes were mostly conserved among the three maize inbreds except for a few DSB-repair/meiotic genes. The findings that the molecular players in limiting class I CO formation (once CO assurance is achieved) were up-regulated and those involved in promoting class II CO formation were down-regulated in CML228 agree with the lower chiasmata number observed in CML228 previously. In addition, epigenetics such as chromatin remodeling and histone modification might play a role. Transport and energy-related processes was up-regulated and Cyclin13 was down-regulated in CML228. The direction of gene expression of these processes agree with that previously found in meiotic tissues compared with vegetative tissues. In summary, we used different natural maize inbred lines from different climatic conditions and have shown their differences in expression landscape in male meiocytes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08922-w.
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Affiliation(s)
- Nelson Garcia
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, USA.,Present Address: Sound Agriculture, 5858 Horton St, Emeryville, CA, USA
| | - Lu Yin
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Stefanie Dukowic-Schulze
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, USA.,Microvascular Biology and Pathobiology, University of Heidelberg, Mannheim, Germany
| | - Claire Milsted
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Penny M A Kianian
- PepsiCo Inc., 210 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, MN, USA
| | - Shahryar Kianian
- Department of Agriculture - Agricultural Research Service, Cereal Disease Lab, U.S., Saint Paul, MN, USA
| | | | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, USA. .,School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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30
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Jiang J, Ou X, Han D, He Z, Liu S, Mao N, Zhang Z, Peng CL, Lai J, Yang C. A diRNA-protein scaffold module mediates SMC5/6 recruitment in plant DNA repair. THE PLANT CELL 2022; 34:3899-3914. [PMID: 35775944 PMCID: PMC9516202 DOI: 10.1093/plcell/koac191] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/21/2022] [Indexed: 06/06/2023]
Abstract
In eukaryotes, the STRUCTURAL MAINTENANCE OF CHROMOSOME 5/6 (SMC5/6) complex is critical to maintaining chromosomal structures around double-strand breaks (DSBs) in DNA damage repair. However, the recruitment mechanism of this conserved complex at DSBs remains unclear. In this study, using Arabidopsis thaliana as a model, we found that SMC5/6 localization at DSBs is dependent on the protein scaffold containing INVOLVED IN DE NOVO 2 (IDN2), CELL DIVISION CYCLE 5 (CDC5), and ALTERATION/DEFICIENCY IN ACTIVATION 2B (ADA2b), whose recruitment is further mediated by DNA-damage-induced RNAs (diRNAs) generated from DNA regions around DSBs. The physical interactions of protein components including SMC5-ADA2b, ADA2b-CDC5, and CDC5-IDN2 result in formation of the protein scaffold. Further analysis indicated that the DSB localization of IDN2 requires its RNA-binding activity and ARGONAUTE 2 (AGO2), indicating a role for the AGO2-diRNA complex in this process. Given that most of the components in the scaffold are conserved, the mechanism presented here, which connects SMC5/6 recruitment and small RNAs, will improve our understanding of DNA repair mechanisms in eukaryotes.
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Affiliation(s)
- Jieming Jiang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Xiaolin Ou
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhipeng He
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Song Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Ning Mao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhonghui Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Chang-Lian Peng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
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31
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Kang S, Guo C, Xue C, Ma C, Mu H, Sun L. Toxic Effects of Two Representative Rare Earth Elements (La and Gd) on Danio rerio Based on Transcriptome Analysis. TOXICS 2022; 10:519. [PMID: 36136485 PMCID: PMC9503537 DOI: 10.3390/toxics10090519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
The expanding applications of rare earth elements (REEs) in various fields have raised concerns about their biosafety. However, previous studies are insufficient to elucidate their toxic effects and mechanisms of action and whether there are uniform or predictable toxicity patterns among REEs. Herein, we investigated the toxic effects of two representative REEs (lanthanum (La) and gadolinium (Gd)) on zebrafish (Danio rerio) through toxicity experiments and transcriptome analysis. The results of the toxicity experiments showed that the two REEs have similar lethality, with half-lethal concentrations (LC50) at micromolar levels and mixed toxicity showing additive effects. Differential expression gene screening and functional group enrichment analysis showed that La and Gd might affect the growth and development of Danio rerio by interfering with some biological molecules. The two REEs showed significant effects on the metabolic pathways of exogenous or endogenous substances, including glutathione sulfotransferase and acetaldehyde dehydrogenase. Moreover, some basic biological processes, such as DNA replication, the insulin signaling pathway, and the p53 signaling pathway, were significantly enriched. Overall, the toxicity patterns of La and Gd may affect some biological processes with different intensities; however, there are many similarities in their toxicity mechanisms and modes of action. The concentrations investigated in this study were comparable to those of REE residues at highly contaminated sites, thus mimicking the ecotoxicological effects at environmentally relevant concentrations.
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Affiliation(s)
- Shu Kang
- School of Public Management, Liaoning University, Shenyang 110016, China
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- School of Environmental and Safety Engineering, Liaoning Petrochemical University, Fushun 113001, China
| | - Cheng Guo
- School of Environmental and Safety Engineering, Liaoning Petrochemical University, Fushun 113001, China
| | - Chenyang Xue
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Chenshu Ma
- School of Public Management, Liaoning University, Shenyang 110016, China
- Liaoning Economic Vocational Technological Institute, Shenyang 110016, China
| | - Huaizhong Mu
- School of Public Management, Liaoning University, Shenyang 110016, China
| | - Lizong Sun
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
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32
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Siqueira JA, Wakin T, Batista-Silva W, Silva JCF, Vicente MH, Silva JC, Clarindo WR, Zsögön A, Peres LEP, De Veylder L, Fernie AR, Nunes-Nesi A, Araújo WL. A long and stressful day: Photoperiod shapes aluminium tolerance in plants. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128704. [PMID: 35313159 DOI: 10.1016/j.jhazmat.2022.128704] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/06/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Aluminium (Al), a limiting factor for crop productivity in acidic soils (pH ≤ 5.5), imposes drastic constraints for food safety in developing countries. The major mechanisms that allow plants to cope with Al involve manipulations of organic acids metabolism and DNA-checkpoints. When assumed individually both approaches have been insufficient to overcome Al toxicity. On analysing the centre of origin of most cultivated plants, we hypothesised that day-length seems to be a pivotal agent modulating Al tolerance across distinct plant species. We observed that with increasing distance from the Equator, Al tolerance decreases, suggesting a relationship with the photoperiod. We verified that long-day (LD) species are generally more Al-sensitive than short-day (SD) species, whereas genetic conversion of tomato for SD growth habit boosts Al tolerance. Reduced Al tolerance correlates with DNA-checkpoint activation under LD. Furthermore, DNA-checkpoint-related genes are under positive selection in Arabidopsis accessions from regions with shorter days, suggesting that photoperiod act as a selective barrier for Al tolerance. A diel regulation and genetic diversity affect Al tolerance, suggesting that day-length orchestrates Al tolerance. Altogether, photoperiodic control of Al tolerance might contribute to solving the historical obstacle that imposes barriers for developing countries to reach a sustainable agriculture.
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Affiliation(s)
- João Antonio Siqueira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Thiago Wakin
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Willian Batista-Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - José Cleydson F Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Matheus H Vicente
- Laboratory of Hormonal Control of Plant Development. Departamento de Ciências Biológicas (LCB), Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Jéssica C Silva
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Wellington R Clarindo
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Lazaro E P Peres
- Laboratory of Hormonal Control of Plant Development. Departamento de Ciências Biológicas (LCB), Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
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33
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Tao R, Wang Y, Jiao Y, Hu Y, Li L, Jiang L, Zhou L, Qu J, Chen Q, Yao S. Bi-PE: bi-directional priming improves CRISPR/Cas9 prime editing in mammalian cells. Nucleic Acids Res 2022; 50:6423-6434. [PMID: 35687127 PMCID: PMC9226529 DOI: 10.1093/nar/gkac506] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
Prime editors consisting of Cas9-nickase and reverse transcriptase enable targeted precise editing of small DNA pieces, including all 12 kinds of base substitutions, insertions and deletions, while without requiring double-strand breaks or donor templates. Current optimized prime editing strategy (PE3) uses two guide RNAs to guide the performance of prime editor. One guide RNA carrying both spacer and templating sequences (pegRNA) guides prime editor to produce ssDNA break and subsequent extension, and the other one produces a nick in the complementary strand. Here, we demonstrated that positioning the nick sgRNA nearby the templating sequences of the pegRNA facilitated targeted large fragment deletion and that engineering both guide RNAs to be pegRNAs to achieve bi-direction prime editing (Bi-PE) further increase the efficiency by up to 16 times and improved the accuracy of editing products by 60 times. In addition, we showed that Bi-PE strategy also increased the efficiency of simultaneous conversion of multiple bases but not single base conversion over PE3. In conclusion, Bi-PE strategy expanded the editing scope and improved the efficiency and the accuracy of prime editing system, which might have a wide range of potential applications.
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Affiliation(s)
- Rui Tao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Yanhong Wang
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Yaoge Jiao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Yun Hu
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Li Li
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Lurong Jiang
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Lifang Zhou
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Junyan Qu
- Center of Infectious Disease, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Qiang Chen
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Shaohua Yao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
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34
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Chen G, Zheng D, Feng N, Zhou H, Mu D, Zhao L, Shen X, Rao G, Meng F, Huang A. Physiological mechanisms of ABA-induced salinity tolerance in leaves and roots of rice. Sci Rep 2022; 12:8228. [PMID: 35581217 PMCID: PMC9114345 DOI: 10.1038/s41598-022-11408-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/21/2022] [Indexed: 11/12/2022] Open
Abstract
Abscisic acid (ABA) plays a crucial role in response to abiotic stress as important small molecules in regulating metabolism. This study aimed to evaluate the ability of foliar spraying ABA to regulate growth quality at rice seedling stage under salt stress. Results demonstrated that salt stress strongly reduced all the growth parameters of two rice seedlings (‘Chaoyouqianhao’ and ‘Huanghuazhan’), caused prominent decrease in the levels of photosynthetic pigments (mainly in Huanghuazhan), photosynthesis and fluorescence parameters. Salinity treatment increased the concentration of malondialdehyde (MDA) and hydrogen peroxide (H2O2) in roots, whereas significant decreased H2O2 was found in leaves of Huanghuazhan. Additionally, salinity triggered high Na+ content particularly in leaves and enhanced catalase (CAT) activities, ascorbate peroxidase (APX) and peroxidase (POD) activities of the two rice seedlings. Nevertheless, salinity-induced increased root ascorbic acid (AsA) and glutathione (GSH) levels while decreased in leaves, which depended on treatment time. Conversely, ABA application partially or completely mitigated salinity toxicity on the seedlings. ABA could reverse most of the changed physiological parameters triggered by salt stress. Specially, ABA treatment improved antioxidant enzyme levels and significantly reduced the Na+ content of two varieties as well as increased the K+, Mg2+ and Ca2+ content in leaves and roots. ABA treatment increased the hormone contents of 1-aminocclopropane carboxylic acid (ACC), trans-zeatin (TZ), N6-isopentyladenosine (IPA), Indole-3-acetic acid (IAA), and ABA in leaves of two rice varieties under salt stress. It is suggested that ABA was beneficial to protect membrane lipid peroxidation, the modulation of antioxidant defense systems and endogenous hormonal balance with imposition to salt stress.
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Affiliation(s)
- Guanjie Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.,South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China. .,Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, 518108, China. .,South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China.
| | - Naijie Feng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China. .,Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, 518108, China. .,South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China.
| | - Hang Zhou
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.,South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China.,School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Dewei Mu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.,South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China
| | - Liming Zhao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.,Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, 518108, China.,South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China
| | - Xuefeng Shen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.,Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, 518108, China.,South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China
| | - Gangshun Rao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.,Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, 518108, China.,South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China
| | - Fengyan Meng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.,South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China
| | - Anqi Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.,South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China
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35
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Siqueira JA, Silva MF, Wakin T, Nunes-Nesi A, Araújo WL. Metabolic and DNA checkpoints for the enhancement of Al tolerance. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128366. [PMID: 35168102 DOI: 10.1016/j.jhazmat.2022.128366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/04/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Acidic soils are a major limiting factor for food production in many developing countries. High concentrations of soluble Al cations, particularly Al3+, inhibit cell division and root elongation in plants. Al3+ damages several biomolecules, including DNA, impairing gene expression and cell cycle progression. Notably, the loss-of-function mutants of DNA checkpoints may mediate Al tolerance. Furthermore, mitochondrial organic acids play key roles in neutralizing Al3+ within the cell and around the rhizosphere. Here, we provide knowledge synthesis on interactions between checkpoints related to mitochondrial organic acid homeostasis and DNA integrity mediating Al tolerance in land plants. These interactions, coupled with remarkable advances in tools related to metabolism and cell cycle, may facilitate the development of next-generation productive crops under Al toxicity.
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Affiliation(s)
- João Antonio Siqueira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Marcelle Ferreira Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Thiago Wakin
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil.
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36
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Giustozzi M, Freytes SN, Jaskolowski A, Lichy M, Mateos J, Falcone Ferreyra ML, Rosano GL, Cerdán P, Casati P. Arabidopsis mediator subunit 17 connects transcription with DNA repair after UV-B exposure. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1047-1067. [PMID: 35220621 DOI: 10.1111/tpj.15722] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Mediator 17 (MED17) is a subunit of the Mediator complex that regulates transcription initiation in eukaryotic organisms. In yeast and humans, MED17 also participates in DNA repair, physically interacting with proteins of the nucleotide excision DNA repair system, but this function in plants has not been investigated. We studied the role of MED17 in Arabidopsis plants exposed to UV-B radiation. Our results demonstrate that med17 and OE MED17 plants have altered responses to UV-B, and that MED17 participates in various aspects of the DNA damage response (DDR). Comparison of the med17 transcriptome with that of wild-type (WT) plants showed that almost one-third of transcripts with altered expression in med17 plants were also changed by UV-B exposure in WT plants. Increased sensitivity to DNA damage after UV-B in med17 plants could result from the altered regulation of UV-B responsive transcripts but MED17 also physically interacts with DNA repair proteins, suggesting a direct role of this Mediator subunit during repair. Finally, we show that MED17 is necessary to regulate the DDR activated by ataxia telangiectasia and Rad3 related (ATR), and that programmed cell death 5 (PDCD5) overexpression reverts the deficiencies in DDR shown in med17 mutants. Our data demonstrate that MED17 is an important regulator of DDR after UV-B irradiation in Arabidopsis.
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Affiliation(s)
- Marisol Giustozzi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), CONICET, Universidad Nacional de Rosario, 2000, Rosario, Argentina
| | | | - Aime Jaskolowski
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Micaela Lichy
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Julieta Mateos
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - María Lorena Falcone Ferreyra
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), CONICET, Universidad Nacional de Rosario, 2000, Rosario, Argentina
| | - Germán L Rosano
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biologia Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, 2000, Rosario, Argentina
| | - Pablo Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula Casati
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), CONICET, Universidad Nacional de Rosario, 2000, Rosario, Argentina
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37
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Wang X, Wang L, Huang Y, Deng Z, Li C, Zhang J, Zheng M, Yan S. A plant-specific module for homologous recombination repair. Proc Natl Acad Sci U S A 2022; 119:e2202970119. [PMID: 35412914 PMCID: PMC9169791 DOI: 10.1073/pnas.2202970119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Homologous recombination repair (HR) is an error-free DNA damage repair pathway to maintain genome stability and a basis of gene targeting using genome-editing tools. However, the mechanisms of HR in plants are still poorly understood. Through genetic screens for DNA damage response mutants (DDRM) in Arabidopsis, we find that a plant-specific ubiquitin E3 ligase DDRM1 is required for HR. DDRM1 contains an N-terminal BRCT (BRCA1 C-terminal) domain and a C-terminal RING (really interesting new gene) domain and is highly conserved in plants including mosses. The ddrm1 mutant is defective in HR and thus is hypersensitive to DNA-damaging reagents. Biochemical studies reveal that DDRM1 interacts with and ubiquitinates the transcription factor SOG1, a plant-specific master regulator of DNA damage responses. Interestingly, DDRM1-mediated ubiquitination promotes the stability of SOG1. Consistently, genetic data support that SOG1 functions downstream of DDRM1. Our study reveals that DDRM1-SOG1 is a plant-specific module for HR and highlights the importance of ubiquitination in HR.
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Affiliation(s)
- Xuanpeng Wang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lili Wang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongchi Huang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhiping Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Cunliang Li
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Zhang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingxi Zheng
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shunping Yan
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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38
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Sugimoto K, Zager JJ, Aubin BS, Lange B, Howe GA. Flavonoid deficiency disrupts redox homeostasis and terpenoid biosynthesis in glandular trichomes of tomato. PLANT PHYSIOLOGY 2022; 188:1450-1468. [PMID: 34668550 PMCID: PMC8896623 DOI: 10.1093/plphys/kiab488] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/23/2021] [Indexed: 05/11/2023]
Abstract
Glandular trichomes (GTs) are epidermal structures that provide the first line of chemical defense against arthropod herbivores and other biotic threats. The most conspicuous structure on leaves of cultivated tomato (Solanum lycopersicum) is the type-VI GT (tVI-GT), which accumulates both flavonoids and volatile terpenoids. Although these classes of specialized metabolites are derived from distinct metabolic pathways, previous studies with a chalcone isomerase 1 (CHI1)-deficient mutant called anthocyanin free (af) showed that flavonoids are required for terpenoid accumulation in tVI-GTs. Here, we combined global transcriptomic and proteomic analyses of isolated trichomes as a starting point to show that the lack of CHI1 is associated with reduced levels of terpenoid biosynthetic transcripts and enzymes. The flavonoid deficiency in af trichomes also resulted in the upregulation of abiotic stress-responsive genes associated with DNA damage and repair. Several lines of biochemical and genetic evidence indicate that the terpenoid defect in af mutants is specific for the tVI-GT and is associated with the absence of bulk flavonoids rather than loss of CHI1 per se. A newly developed genome-scale model of metabolism in tomato tVI-GTs helped identify metabolic imbalances caused by the loss of flavonoid production. We provide evidence that flavonoid deficiency in this cell type leads to increased production of reactive oxygen species (ROS), which may impair terpenoid biosynthesis. Collectively, our findings support a role for flavonoids as ROS-scavenging antioxidants in GTs.
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Affiliation(s)
- Koichi Sugimoto
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Jordan J Zager
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington, 99164-7411, USA
| | - Brian St Aubin
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Bernd Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington, 99164-7411, USA
| | - Gregg A Howe
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, 48824, USA
- Author for communication:
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39
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Allen JR, Wilkinson EG, Strader LC. Creativity comes from interactions: modules of protein interactions in plants. FEBS J 2022; 289:1492-1514. [PMID: 33774929 PMCID: PMC8476656 DOI: 10.1111/febs.15847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/06/2021] [Accepted: 03/26/2021] [Indexed: 01/03/2023]
Abstract
Protein interactions are the foundation of cell biology. For robust signal transduction to occur, proteins interact selectively and modulate their behavior to direct specific biological outcomes. Frequently, modular protein interaction domains are central to these processes. Some of these domains bind proteins bearing post-translational modifications, such as phosphorylation, whereas other domains recognize and bind to specific amino acid motifs. Other modules act as diverse protein interaction scaffolds or can be multifunctional, forming head-to-head homodimers and binding specific peptide sequences or membrane phospholipids. Additionally, the so-called head-to-tail oligomerization domains (SAM, DIX, and PB1) can form extended polymers to regulate diverse aspects of biology. Although the mechanism and structures of these domains are diverse, they are united by their modularity. Together, these domains are versatile and facilitate the evolution of complex protein interaction networks. In this review, we will highlight the role of select modular protein interaction domains in various aspects of plant biology.
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Affiliation(s)
- Jeffrey R. Allen
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
| | - Edward G. Wilkinson
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
| | - Lucia C. Strader
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
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40
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DNA Double-Strand Break Repairs and Their Application in Plant DNA Integration. Genes (Basel) 2022; 13:genes13020322. [PMID: 35205367 PMCID: PMC8871565 DOI: 10.3390/genes13020322] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 01/25/2023] Open
Abstract
Double-strand breaks (DSBs) are considered to be one of the most harmful and mutagenic forms of DNA damage. They are highly toxic if unrepaired, and can cause genome rearrangements and even cell death. Cells employ two major pathways to repair DSBs: homologous recombination (HR) and non-homologous end-joining (NHEJ). In plants, most applications of genome modification techniques depend on the development of DSB repair pathways, such as Agrobacterium-mediated transformation (AMT) and gene targeting (GT). In this paper, we review the achieved knowledge and recent advances on the DNA DSB response and its main repair pathways; discuss how these pathways affect Agrobacterium-mediated T-DNA integration and gene targeting in plants; and describe promising strategies for producing DSBs artificially, at definite sites in the genome.
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41
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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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42
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Ishikawa M, Hasebe M. Molecular mechanisms of reprogramming of differentiated cells into stem cells in the moss Physcomitrium patens. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102123. [PMID: 34735974 DOI: 10.1016/j.pbi.2021.102123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/14/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Plant and animal stem cells can self-renew and give rise to differentiated cells to form tissues or organs. Unlike differentiated cells in animals, those in land plants can be readily reprogrammed into stem cells, reflecting the plasticity of plant cell identity. The moss Physcomitrium patens (synonym: Physcomitrella patens) is highly regenerable, and its leaf cells can be reprogrammed into stem cells in response to wounding or by transient DNA damage without wounding. Wounding and DNA damage induce STEM CELL-INDUCING FACTOR 1, an APETALA2/ETHYLENE RESPONSE FACTOR. Here, we summarize the genetic networks that regulate cellular reprogramming in P. patens and the roles of STEMIN1 and discuss the generality and divergence of the molecular mechanisms underlying cellular reprogramming in land plants and animals.
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Affiliation(s)
- Masaki Ishikawa
- National Institute for Basic Biology, Okazaki, 444-8585, Japan; School of Life Science, The Graduate University for Advanced Studies, Okazaki, 444-8585, Japan.
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, 444-8585, Japan; School of Life Science, The Graduate University for Advanced Studies, Okazaki, 444-8585, Japan.
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43
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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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44
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Wang Q, La Y, Xia H, Zhou S, Zhai Z, La H. Roles of MEM1 in safeguarding Arabidopsis genome against DNA damage, inhibiting ATM/SOG1-mediated DNA damage response, and antagonizing global DNA hypermethylation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:87-104. [PMID: 34859586 DOI: 10.1111/jipb.13200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
Arabidopsis methylation elevated mutant 1 (mem1) mutants have elevated levels of global DNA methylation. In this study, such mutant alleles showed increased sensitivity to methyl methanesulfonate (MMS). In mem1 mutants, an assortment of genes engaged in DNA damage response (DDR), especially DNA-repair-associated genes, were largely upregulated without MMS treatment, suggestive of activation of the DDR pathway in them. Following MMS treatment, expression levels of multiple DNA-repair-associated genes in mem1 mutants were generally lower than in Col-0 plants, which accounted for the MMS-sensitive phenotype of the mem1 mutants. A group of DNA methylation pathway genes were upregulated in mem1 mutants under non-MMS-treated conditions, causing elevated global DNA methylation, especially in RNA-directed DNA methylation (RdDM)-targeted regions. Moreover, MEM1 seemed to help ATAXIA-TELANGIECTASIA MUTATED (ATM) and/or SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) to fully activate/suppress transcription of a subset of genes regulated simultaneously by MEM1 and ATM and/or SOG1, because expression of such genes decreased/increased consistently in mem1 and atm and/or sog1 mutants, but the decreases/increases in the mem1 mutants were not as dramatic as in the atm and/or sog1 mutants. Thus, our studies reveals roles of MEM1 in safeguarding genome, and interrelationships among DNA damage, activation of DDR, DNA methylation/demethylation, and DNA repair.
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Affiliation(s)
- Qianqian Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yumei La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huihui Xia
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaoxia Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhaoyu Zhai
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, 210095, China
| | - Honggui La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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Sheridan ML, Simonelli L, Giustozzi M, Casati P. Ultraviolet-B Radiation Represses Primary Root Elongation by Inhibiting Cell Proliferation in the Meristematic Zone of Arabidopsis Seedlings. FRONTIERS IN PLANT SCIENCE 2022; 13:829336. [PMID: 35401611 PMCID: PMC8988989 DOI: 10.3389/fpls.2022.829336] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/28/2022] [Indexed: 05/13/2023]
Abstract
In Arabidopsis thaliana plants, exposure to UV-B induces an inhibition of primary root elongation. Different mutants have been isolated that are deficient in this response; however, little is known about the cellular and molecular mechanisms that regulate inhibition of root elongation in seedlings exposed to UV-B. In this work, we investigated the effect UV-B irradiation of different organs on primary root elongation. Our results demonstrate that irradiation of the leaves and shoots only induce a partial inhibition of primary root elongation, while when only roots are exposed to this radiation, primary root inhibition is similar as that measured when the complete seedling is irradiated. The consequences of exposure at different root developmental stages and times after the end of the treatment was also studied. We here show that inhibition of primary root elongation is a consequence of a decrease in cell proliferation in the meristematic zone of the primary roots, while the elongation zone size is not affected by the treatment. The decrease in cell number after UV-B exposure is partially compensated by an increase in cell length in the root meristem; however, this compensation is not enough to maintain the meristem size. We also here demonstrate that, similarly as what occurs in developing leaves, GROWTH REGULATING FACTOR 3 (GRF3) transcription factor regulates cell proliferation in UV-B irradiated roots; however, and in contrast to what occurs in the leaves, this response does not depend on the presence of MITOGEN ACTIVATED PROTEIN KINASE 3 (MPK3). Inhibition of primary root elongation by UV-B under our experimental conditions is also independent of the UV-B photoreceptor UV RESISTANT LOCUS 8 (UVR8) or ATAXIA TELANGIECTASIA MUTATED (ATM); but a deficiency in ATM AND RAD3-RELATED (ATR) expression increases UV-B sensitivity in the roots. Finally, our data demonstrate that UV-B affects primary root growth in various Arabidopsis accessions, showing different sensitivities to this radiation.
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Liang W, Li J, Sun L, Liu Y, Lan Z, Qian W. Deciphering the synergistic and redundant roles of CG and non-CG DNA methylation in plant development and transposable element silencing. THE NEW PHYTOLOGIST 2022; 233:722-737. [PMID: 34655488 PMCID: PMC9298111 DOI: 10.1111/nph.17804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 10/11/2021] [Indexed: 05/10/2023]
Abstract
DNA methylation plays key roles in transposable element (TE) silencing and gene expression regulation. DNA methylation occurs at CG, CHG and CHH sequence contexts in plants. However, the synergistic and redundant roles of CG and non-CG methylation are poorly understood. By introducing CRISPR/Cas9-induced met1 mutation into the ddcc (drm1 drm2 cmt2 cmt3) mutant, we attempted to knock out all five DNA methyltransferases in Arabidopsis and then investigate the synergistic and redundant roles of CG and non-CG DNA methylation. We found that the homozygous ddcc met1 quintuple mutants are embryonically lethal, although met1 and ddcc mutants only display some developmental abnormalities. Unexpectedly, the ddcc met1 quintuple mutations only reduce transmission through the male gametophytes. The ddcc met1+/- mutants show apparent size divergence, which is not associated with difference in DNA methylation patterns, but associated with the difference in the levels of DNA damage. Finally, we show that a group of TEs are specifically activated in the ddcc met1+/- mutants. This work reveals that CG and non-CG DNA methylation synergistically and redundantly regulate plant reproductive development, vegetative development and TE silencing in Arabidopsis. Our findings provide insights into the roles of DNA methylation in plant development.
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Affiliation(s)
- Wenjie Liang
- State Key Laboratory of Protein and Plant Gene ResearchPeking‐Tsinghua Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing100871China
| | - Jinchao Li
- State Key Laboratory of Protein and Plant Gene ResearchPeking‐Tsinghua Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing100871China
- School of Advanced Agricultural SciencesPeking UniversityBeijing100871China
| | - Linhua Sun
- School of Advanced Agricultural SciencesPeking UniversityBeijing100871China
| | - Yi Liu
- State Key Laboratory of Protein and Plant Gene ResearchPeking‐Tsinghua Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing100871China
| | - Zijun Lan
- State Key Laboratory of Protein and Plant Gene ResearchPeking‐Tsinghua Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing100871China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene ResearchPeking‐Tsinghua Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing100871China
- School of Advanced Agricultural SciencesPeking UniversityBeijing100871China
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Prochazkova K, Finke A, Tomaštíková ED, Filo J, Bente H, Dvořák P, Ovečka M, Šamaj J, Pecinka A. Zebularine induces enzymatic DNA-protein crosslinks in 45S rDNA heterochromatin of Arabidopsis nuclei. Nucleic Acids Res 2021; 50:244-258. [PMID: 34904670 PMCID: PMC8754632 DOI: 10.1093/nar/gkab1218] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/01/2021] [Indexed: 11/14/2022] Open
Abstract
Loss of genome stability leads to reduced fitness, fertility and a high mutation rate. Therefore, the genome is guarded by the pathways monitoring its integrity and neutralizing DNA lesions. To analyze the mechanism of DNA damage induction by cytidine analog zebularine, we performed a forward-directed suppressor genetic screen in the background of Arabidopsis thaliana zebularine-hypersensitive structural maintenance of chromosomes 6b (smc6b) mutant. We show that smc6b hypersensitivity was suppressed by the mutations in EQUILIBRATIVE NUCLEOSIDE TRANSPORTER 3 (ENT3), DNA METHYLTRANSFERASE 1 (MET1) and DECREASE IN DNA METHYLATION 1 (DDM1). Superior resistance of ent3 plants to zebularine indicated that ENT3 is likely necessary for the import of the drug to the cells. Identification of MET1 and DDM1 suggested that zebularine induces DNA damage by interference with the maintenance of CG DNA methylation. The same holds for structurally similar compounds 5-azacytidine and 2-deoxy-5-azacytidine. Based on our genetic and biochemical data, we propose that zebularine induces enzymatic DNA–protein crosslinks (DPCs) of MET1 and zebularine-containing DNA in Arabidopsis, which was confirmed by native chromatin immunoprecipitation experiments. Moreover, zebularine-induced DPCs accumulate preferentially in 45S rDNA chromocenters in a DDM1-dependent manner. These findings open a new avenue for studying genome stability and DPC repair in plants.
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Affiliation(s)
| | | | - Eva Dvořák Tomaštíková
- Institute of Experimental Botany, The Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900 Olomouc, Czech Republic
| | - Jaroslav Filo
- Institute of Experimental Botany, The Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900 Olomouc, Czech Republic
| | - Heinrich Bente
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Petr Dvořák
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Miroslav Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Ales Pecinka
- To whom correspondence should be addressed. Tel: +420 585 238 709;
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48
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García-Caparrós P, De Filippis L, Gul A, Hasanuzzaman M, Ozturk M, Altay V, Lao MT. Oxidative Stress and Antioxidant Metabolism under Adverse Environmental Conditions: a Review. THE BOTANICAL REVIEW 2021; 87:421-466. [PMID: 0 DOI: 10.1007/s12229-020-09231-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/01/2020] [Indexed: 05/25/2023]
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49
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Youssef OA, Tammam AA, El-Bakatoushi RF, Alframawy AM, Emara MM, El-Sadek LM. Uptake of hematite nanoparticles in maize and their role in cell cycle dynamics, PCNA expression and mitigation of cadmium stress. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:1177-1189. [PMID: 34374200 DOI: 10.1111/plb.13315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/24/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Cadmium toxicity is considered a major threat to several crops worldwide. Hematite nanoparticles (NPs), due to their small size and large specific surface area, could be applied as an adsorbent for toxic heavy metals in soil. Also, they serve as an efficient nano-fertilizer, promoting Fe availability and biomass production in plants, thus enabling Cd2+ -induced stress tolerance. The phytotoxicity of five different concentrations of hematite NPs, ranging from 500 to 8,000 mg·kg-1 , and Cd2+ concentrations (110 or 130 mg·kg-1 Cd2+ ) alone or combined with 500 mg·kg-1 NPs was evaluated in maize. The changes in fresh weight, element analysis, cell cycle regulation, DNA banding patterns and proliferating cell nuclear antigen (PCNA) expression were used as biomarkers. The results revealed that increased fresh weight and fewest polymorphic DNA bands were detectable after treatment with 500 mg·kg-1 NPs. However, at 8,000 mg·kg-1 NPs, PCNA expression increased significantly, which resulted in cell cycle arrest at the G1/S checkpoint in roots. Significant reductions in fresh weight, altered nutrient profiles and cell cycle perturbations are considered symptoms of Cd2+ toxicity in maize. Conversely, amending 500 mg·kg-1 NPs with 130 mg·kg-1 Cd2+ increased fresh weight, Fe concentration and genomic template stability, while reducing Cd2+ uptake and PCNA1 expression. Overall, 8,000 mg·kg-1 hematite NPs interfered with the cellular homeostatic balance of maize, resulting in a cascade of genotoxic events, leading to growth inhibition. Although 500 mg·kg-1 hematite NPs alleviated Cd2+ -induced DNA damage to a certain extent, their impact on cell cycle progression requires further verification.
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Affiliation(s)
- O A Youssef
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Camp Caesar, 21525, Egypt
| | - A A Tammam
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Camp Caesar, 21525, Egypt
| | - R F El-Bakatoushi
- Biology and Geology Sciences Department, Faculty of Education, Alexandria University, Alexandria, El-shatby, 526, Egypt
| | - A M Alframawy
- Nucleic Acids Research Department, Genetic Engineering & Biotechnology Research Institute (GEBRI), City for Scientific Research and Technological Applications, Alexandria, Borg El-Arab, 21933, Egypt
| | - M M Emara
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Ibrahimia, 21321, Egypt
| | - L M El-Sadek
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Camp Caesar, 21525, Egypt
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50
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Saini S, Kaur N, Pati PK. Phytohormones: Key players in the modulation of heavy metal stress tolerance in plants. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 223:112578. [PMID: 34352573 DOI: 10.1016/j.ecoenv.2021.112578] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 05/07/2023]
Abstract
Heavy metal (HM) stress in plants has received considerable global attention as it threatens sustainable growth in agriculture worldwide. Hence, desperate efforts have been undertaken for combating the effects of this stress in plants. Interestingly, the use of phytohormones in reducing the impact of HM toxicity has gained much momentum in the recent past. Phytohormones act as chemical messengers that improve the HM stress resistance in plants, thus allowing them to retain their growth and developmental plasticity. Their exogenous application as well as manipulation of endogenous levels through precise targeting of their biosynthesis/signaling components is a promising approach for providing a protective shield against HM stress in plants. However, for the successful use of phytohormones for field plants exposed to HM toxicity, in-depth knowledge of the key pathways regulated by them is of prime importance. Hence, the present review mainly summarizes the key conceptual developments on the involvement of phytohormones in the mitigation of HM stress in plants. The role of various genes, proteins, and signaling components involved in phytohormones associated HM stress tolerance and their modulation has also been discussed. Thus, this update will pave the way for improving HM stress tolerance in plants with the advent of phytohormones for sustainable agriculture growth in the future.
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Affiliation(s)
- Shivani Saini
- Department of Botany, GGDSD College, Sector-32C, Chandigarh, India.
| | - Navdeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India; Centre for Agricultural Research and Innovation, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India; Centre for Agricultural Research and Innovation, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
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